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I've noticed only after I already made a post on the new videoproduction/ video.stackexchange site that the official site of FFmpeg's contact page actually points to HERE (Super User site, with tags of ffmpeg) - clicking the tag shows that FFmpeg questions posted here do not show up there, and similarly tags there do not show up here.

Is there a reason for having it all so separated up when people searching for FFmpeg here would probably want to see questions posted in both the video and sound.stackexchange sites rather than hiding those posts?

So we have a situation where the official site is saying post on Super User, but Stack Exchange and search engines are guiding people towards the video Stack Exchange site which isn't linked to officially. Should there really be this much separation, and which one should be used?

(I don't know if site admin are active in any of the discussions though. I get the impression there's no say of the community in how the site is run compared to how wikis tend to be. I thought about posting this on the meta site, but I figure people who care about FFmpeg stuff are more likely to see it here.)

is there a reason for having it all so separated

Video Production and Sound Design are both beta websites. Super User is one of the first Stack Exchange communities. However, all three are separate communities, and questions that appear in one do not appear in the others on purpose.

So we have a situation where the official site is saying post on Super User, but Stack Exchange and search engines are guiding people towards the video Stack Exchange site

The Stack Exchange community has no control over which community the author of FFMPEG recommends. However, a question about FFMPEG is currently within scope, at all three communities. However, every question about FFMPEG isn't necessarily within scope, at a given community. The help center of a given community provides the necessary guidance to determine if a question should be submitted.

I get the impression there's no say of the community in how the site is run compared to how wikis tend to be. I thought about posting this on the meta site, but I figure people who care about FFmpeg stuff are more likely to see it here.

A Stack Exchange community does indeed have input into what should be within scope. This is the point of the community having a Beta phase, in order to establish what will or won't be within scope. Super User is already an established website. What applies to Video Production and Sound Design does not necessarily apply to Super User.

is there a reason for having it all so separated up when people searching for ffmpeg here would probably want to see questions posted in both the Video Production and Sound Design rather than hiding those posts?

The questions are not hidden, if they were not submitted at a given community, they don't even exist in the other communities.

Why so many different sites?

As one of the local FFmpeg “top users”¹ who sometimes visits other sites to look at FFmpeg questions, let me just say that I also find the fragmentation a little bit disadvantageous, if not annoying sometimes. It makes it hard to monitor interesting questions, and we cannot close a question as a duplicate of another question that happens to be on another site.

Now, the reason the FFmpeg project points to Super User is—I assume—that one of the main FFmpeg contributors for community and documentation is also very active here.

Stack Exchange allows different communities to be created, and it's only natural that these may have overlapping scope. There's no reason for FFmpeg to have its own Q&A site, so these posts now are spread all over the SE network.

Does it matter?

I also have to disagree that VIdeo Production and Sound Design are the main sites that people find when looking for FFmpeg problems. In fact, it's probably all of the Stack Exchange sites that come up as relevant from a web search.

So in essence, for users wanting to find help, it should not matter much. Perhaps there's a barrier to asking questions in a community that you don't know, but overall I think the FFmpeg help ecosystem on Stack Exchange is quite good, and also up-to-date (compared to many outdated blog articles or mailing list messages).

Where should I ask then?

There is a clear distinction between some aspects of FFmpeg that make a question on- or off-topic for Super User and Video Production, but not for Stack Overflow, or vice-versa. FFmpeg used as a programming library is off topic here, but on topic on Stack Overflow. FFmpeg used as a command-line tool is off topic on Stack Overflow, but on topic here.²

If your question is on topic in a given community, feel free to post it wherever you feel most welcome.

I happen to post (most of my) questions here, but sometimes I feel like another community is more appropriate. Anyway, if your question does not get an answer, you can have it migrated to another site, if you wish so.

_{¹ Not bragging, just for context.
² This is not always as strictly enforced, and you'll find lots of CLI questions over on Stack Overflow.}

Super User was added instead of Video Production because the former has greater traffic - no other reason.

I think of Super User as a fallthrough site. Its help states

Super User is for computer enthusiasts and power users. If you have a
question about …

computer hardware,

computer software, or

personal and home computer networking

and it is not about …

That's like saying, "This site is for everything but not ...". Since the scope of the site is basically carved by negative definitions, questions end up here if there isn't a dedicated sister site or the user is new or dropped off by Google.

I would actually recommend Video.SE now because, outside of the top users for the ffmpeg tag, that community will have more experience with ffmpeg than the general audience of Super User. Since it also has less traffic, a new question will float at the top for more time than at Super User. FFmpeg is a tool to manipulate video and audio, and between SU and Video.SE, the latter is a better fit.

All that said, in practice, it doesn't make much of a difference as it's the same small group of users who engage with most questions.