I finally updated my Switch to 9.0.1 and PFBA 3.4 works just fine, controls work perfectly for me. I have no clue why people are reporting that it doesn't work on new firmware. It works just fine.
Here's where I got it:
https://github.com/Cpasjuste/pemu/releases
Here's where I got it:
https://github.com/Cpasjuste/pemu/releases