Just a quick update on the situation.
As barbudreadmon recommended I updated my romset for the games that would run only with the pifba emulator and now I can play them with the lr-fbalpha emulator! Which again doesn't need any further controller settings since I had everything done already.
It did not solve my issue with the pifba but updating the romset made it unnecessary to fix.

Thanks again for the quick help. I think I'll go grab a beer and start playing.
Cheers.