Currently it’s set to Select+Start by default but I’d like to change it to Select+R3 on my ps3 controller. This is the button combo I use for all other emulators.

Edit: It appears this fork here will do it: https://github.com/recalbox/pifba

Edit 2: I’ve just tested it and it works great. Was able to change the hotkey button to R3 and the quit button to select.