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Let's say I got a Master's degree in Computer Science with a thesis in machine learning (focused on molecular modeling). If I was later accepted into a paid Research Assistantship (not as a student) where I built machine learning models for a laboratory, and this lasted for at least a couple years:

Would employers wanting a machine learning engineer / software engineer view this as valid work experience?

If not, assuming I had entry level experience, how would employers view a 2-3 year gap away from industry where I worked as a research assistant but decided to go back to industry?

It is absolutely valid experience. There are R&D positions pretty much mirroring academic research assistant positions in the industry. Also, if you built machine learning models as part of your work this is great experience. Biggest demand in data science is towards people who have experience with the logical portions of the work, not just people with experience using some black box libraries.

Also, this demand is not towards people who have worked with that specific industry. Any experience dealing with the logic beyond using the newest hottest tool is valid. I have worked with data scientists with backgrounds in aerospace working at a travel company or with biotech backgrounds working for a power company, in senior positions.

I would say definitely put it on there and you will be in absolute great shape.