PPSSPP seems to have its own configuration settings that you can access by pressing the ESC button on a keyboard. I was able to remap controls correctly there. Unfortunately for me, once remapped, the menu registers a constant down press, so the menu becomes unusable afterward. I’m guessing this is part of the “experimental” status of the emulator.
I couldn’t get Reicast to boot any games at all, so I can’t help you there.
No, I’m in the same boat as you – the face buttons map as d-pad, I think the actual d-pad maps as hat switches. It’s incorrect but makes the game side usable, at least. I’m using a Logitech F310 on a Pi 2 with berryboot if it helps with diagnosis, though I suspect the issue is unrelated to hardware.
the method they mentioned does fix the issue, i forked the ppsspp github and made the edit. Change the git link in the retropie ppsspp script and recompiled the emulator. I don’t have the controller issue anymore and i can freely edit my controls without issue.