How did you make the alien animations work with AAF?
I never made them work.

That took some extra effort in the form of downloading a mod that makes the alien model an equippable outfit and putting it on companions/settlers so they still acted like humans. They're technically not the actual 'alien' models in the game, they just look like them. Otherwise yeah, I had the same issue with the proper aliens as well since they're only rigged to move like animatronics. Also, the fingers mess up and look weird in a lot of the poses because they bend in ways they weren't meant to, hence why they look pretty odd in some of the images too. I did my best to smooth them out and make it less noticable. haha

The mod can be found on the Nexus website here.