The force that the planetoid and its atmosphere exerts on the balloon is a combination of air pressure and gravity. Assuming that the atmospheric pressure is comparable to Earth's, the pressure on the balloon is 14 lbs/square inch outwards. I have no idea what the weight of a square inch of unobtanium balloon materials is, but since the question has the balloon stay up, we can assume it's less than that, and the balloon can be kept aloft by atmospheric pressure.

Now, ignoring gravity for the moment, consider the tightly inflated balloon. The outward pressure on it is due entirely to the atmospheric pressure at the interior surface of the balloon. And that atmospheric pressure decreases with altitude. So the higher up a piece of the balloon's surface is the lower the outward force from air pressure and the lower the balloon's surface is, the higher the outwards force. This is exactly what's needed to center the balloon.

But how big is the force? That depends on the lapse rate, the rate at which atmospheric pressure declines with altitude. Here the fact that it's a planetoid works against you.

The equation for atmospheric density (or pressure) as a function of height is d = e ^-kgh where k is a constant, g is the surface gravity, and h is the height. A lower gravity means that density (and hence pressure) declines less rapidly with height. The height at which atmospheric pressure drops by half is inversely proportional to the gravitational binding and thus to the mass. The half-height for Earth is about 3.5 miles. Ceres (the largest asteroid in the Solar System) has a mass of 0.0002 Earth, and consequently has a half-height of 17,000 miles. Smaller planetoids would have correspondingly larger half-heights.

So we have a planetoid inside a pressurized balloon of air. The lapse rate of the planetoid is so small that it would make an infinitesimal difference in the atmospheric pressure over the mile from planetoid surface to balloon, and consequently, there would be only a small restoring force tending to keep the balloon centered on the planetoid.

Now bring gravity back into the picture: Since we have assume that the air pressure exerts a greater outward force on the balloon's surface than the inward force due to gravity, we can call the balloon a sphere. Newton himself proved that a uniform spherical shell of matter exerts no net force on an object inside it, and the object inside it naturally exerts not net force on the shell. So as long as the shell is inflated by air pressure, the gravity of the planetoid has no effect, and exerts no restoring force.

Bottom line: You'd have a spherical balloon of air with a planetoid drifting around inside with no particular tendency to stay in the center.

Solar wind will blow the 'wrapper' into the planet

Solar wind is a stream of charged particles blowing from the sun out into space. At a distance of 1 AU, pressure from the charged particles is in the range of 1-6 nPa. This isn't much, but integrated over the surface of a planet this will cause significant deformation of your shell. It will not remain perfectly concentric.

... also, about that solar wind ...

Solar wind is mostly composed of protons. Therefore it is positively charged. If the solar wind impacts on the shell, the shell will eventually be positively charged, since protons will strip off electrons. This will turn your entire system into a giant capacitor. Eventually, the voltage across the capacitor will be high enough and then ...

Does your planet have a magnetic field?

Back on topic, an electrostatically charged shell around your planet is bad for other reasons. Does your planet have a magnetic field like Earth does? Well, then you will get a Lorentz force vector based on the motion of a charged object in a magnetic field. Even if your planet's magnetic field is perfectly symmetrical, the shell won't be, thanks to solar wind, so there will be some asymmetric magnetic forces pulling on the shell.

The direction of the force will vary depending on the magnitude of the magnetic field, the distance the magnetic field extends from the planet, the distance of the shell from the planet, etc. There is also the possibility of relative motion (even if it is minor) between the shell and the planet. All of these factors will be significant, so I'm not prepared to estimate the magnitude or direction of the magnetic force on the solar-wind-charged-shell. But it won't be zero, so your shell is going to move.

Conclusion

The shell is going to hit the planet, one way or another.

Better idea though, what is wrong with using gravity to capture things on the planet's surface? Gravity is, after all, what kept our atmosphere attached to us for the last few billion years. A 'gravity well generator' that you put your planet into to prevent things from leaving the surface isn't any less realistic than magical handwavium shrink wrap on a planet.

Action and reaction

You omit to give a mechanism for construction other than a semi plausible "inflation". As young engineers we joked about "sky hooks" but as with all things formerly implausible, such as space elevators, these are now a reality see wiki. So tethers during construction would aid stability on completion and provide a temporary framework for supporting the outer shell. If the planetoid is mined for obtainium to use for the tethers and shell then the orbit will not change as the total mass is unchanged.

How many tethers are required? Mathematically four (tetrahedral) would be the absolute minimum, diametrically that becomes eight, say a safety factor of three in pairs for redundancy /maintenance then 12 pairs of obtainium to the core (similar to those shown in photo) and 30 obtainium (green) for the lattice should be enough for a blue inflated translucent unobtanium Icosasphere. Which tethered together rotate together Click to see animation by Illustr CC BY-SA 4.0 Note I have truncated top and bottom as more economic and less problematic to produce 2 level platforms

Concept of spherical objects with one suspended inside another**

If inflation during construction is uniform on opposite sides the system will stay self centric.

kingledion raised the issue of solar winds but earth is not pushed into outer space, any additional mass will pull the planetoid inwards etc. Equally if containing conductive strands the lattice frame acts more like a faraday cage (with it own electromagnetic issues, but a wide open lattice will not cause hardship).

kingledion, Mark Olson et al. Have in general pointed out that there are similarities to Newtons shell theory and there would be nothing to stop the planet and shell moving at different rates thus on completion over time the core and case could drift into one another. Using diametrically opposite tethers will stop any such drift.

The "space anchors" would provide an interface for space elevator occupants to transfer to the 12 orbital spacepads, and the lattice could be used for monorail links between them. Given the layout any failure/maintenance would still provide a choice of back-up routes. However due to the spin the shell shape is likely to be squished top and bottom, so 2 polar spaceports would make more sense. To counteract the inward pull at the poles a pillar or stanchion form support is needed as proposed by rek ? these could be triangular in nature to align with the truncated oblate (flattened) spheroid.

What could create a calamitous wobble with a catastrophic collision is significantly uneven internal weather, or a drastic external collision event. Both of these would be mitigated by use of tethers.

In either case with enough force the "skin" could rupture or exceed the tethers strength and the whole system instantly collapse. But then unobtainium is indestructible, per your specification !

I think you will need some kind of alien stabilization technology. Imagine a tennis ball inside a large inflated balloon. The pressure of the air inside will not keep the tennis ball from bouncing around, even in zero gravity. On a planetary scale the rocky planet still needs to spin and orbit its star, so the planet-sized balloon would have to keep up with the orbiting planet, using some kind of propulsion system.

I think a better technique for terraforming is to understand how Earth keeps its own warm atmosphere from leaking out into space. It's really quite simple. It's just gravity. Gravity keeps the air molecules on our planet. Our planet also has a spinning core of molten iron which creates an electromagnetic field around our planet, protecting it from solar winds which might strip away our ozone layer and atmosphere. The aliens would only have to pick a sufficiently massive planet, fill it with their preferred atmosphere, and generate a protective electromagnetic shield. No balloons needed.

Have you ever wrapped a gift for your girlfriend/boyfriend in a balloon?
If you have done it, or have at least seen the thing, you should have noticed that the pressure in the balloon doesn't keep the gift in the middle of the balloon.

You simply have a body immersed in a fluid, which will then experience the usual buoyancy force. Since the planetoid will be subject to the gravitational attraction of the main body (I assume it is the central star), that won't displace the planetoid with respect to the wrapping.

However, your aliens, in order to wrap the planetoid, must have matched its orbital velocity with the velocity of the wrapping. So it is safe to assume that the center of mass of the planetoid and the center of mass of the wrapping are moving in the same way. If they didn't do it, the planetoid will simply burst through the wrap at some km/s. So my suggestion to the alien is: match the orbital velocity of the planetoid! Then orbital mechanics will take care of the rest.

If they didn't bother in setting up a rotational regime coherent with that of the planetoid, what will happen? The atmosphere in the wrap will be initially at rest with respect to the wrapping, except for the layer in contact with the planetoid surface, which will be drag around. This drag will then transfer to the outer layers, until the entire wrap and the enclosed atmosphere spin coherently with the planetoid.

Space.com has an article on that subject.

The idea that small worlds may have insufficient gravity to hold-on to an atmosphere and therefore a shell is necessary. The article did not mention, however, stabilizing the shell around the planet. For that, I have done a thought experiment and I hope you find that clear to follow.

The thought experiment starts with taking a steel ingot. Put it on the water, and it will sink. Now, take that ingot and flatten it, then turn it into a concave plate. Put it on the water, and it will float. A ship made of steel will remain afloat as long as it is not filled with water. Pull it up a bit and leave it, it will drop back to its original height. Push it down a bit and leave it, it will pop-up again to its original height. Now, fill it with water and it will sink. This effect is the result of Archimedes law. Going back to the planet, replace water with an atmosphere, and the air above it with a vacuum. The shell is right between the two.

We now cover the atmosphere with a shell. it is atop the atmosphere. The surface atmospheric pressure is the weight of the atmosphere under the planet's gravity, and as you go up the atmosphere, the pressure goes down. The weight of the shell adds-up to that weight. It presses the air underneath as it tends to go down, until it cannot press it any further. At this point, the upwards pressure counteracts the downward weight of the shell and the shell should stay afloat in balance.

Let's say we pushed the shell on one side. It is like we made a dent on the side we pushed (Remember the concave plate?), and a bulge on the opposite side. If the shell was artificially held in this off-center position, the atmosphere will be moved as well. It will shift to a new equilibrium state and the surface pressure will once again become uniform all-over the planet's surface.

The pressure would go down as you go up, so the lowered section (dent) would experience a stronger upward force than the higher section (bulge) on its Antipodes. The shell will move back to its central position. All the "air columns" of the atmosphere behave like a series of communicating vessels. The shorter air columns (under the dent) will push up the shell at a force, greater than that of the taller columns (under the bulge)

Exceptions

Solar wind would exert some pressure and will drift the shell a bit off-center, but not noticeably when viewed from the surface.

large and small asteroids will not have sufficient gravity to stabilize the shell around the center. It is not necessary to install pillars, cables will be just fine, because the bubble cannot collapse without venting the atmosphere.