No, they are definitely per-AI in terms of the unlocks. The experimental stuff isn't unlocked in the normal way, though, because it's not a bonus ship class. I just looked through the code, and I don't see an immediate way that the situation you describe could result. So most likely they are not being directly seeded there, though I could be wrong.
More likely it's... something else. Regenerator trains, possibly... or maybe something to do with barracks or similar. Or maybe some sort of odd bug that I just am not able to see. If you wouldn't mind logging the save with the issue into mantis, I can take a look and see if I can figure out what it is; having looked in the obvious places so far in the code, I'm not sure what it could be. But, unless something is more broken than I realize, I think it's likely to be limited to just experimentalist ships as the issue, rather than just general unlocks, since as I noted those are two really different types of code branch -- which would make it a less critical issue, though still one to chase down.