Oh wow I forgot I got that part working! If this is a feature you guys are interested in I could give a shot at porting it back. The logic should be mostly the same.
So yeah, our bsatool now has the ability create an empty BSA archive and now add files to it. I would like to be able to add a list of files or give it a directory, that can be a follow up Issue/MR, this this is a great step forward.
I also created a new Issue that tracks ba2 support.