not sure how to send private message.
but on the FAQ you posted,
the (hot keys dont work with dolphin)
there may be a related issue, where, controller one gets set to player 2, and controller 2 gets set to player 1 in dolphin.
also, when having a keyboard plugged in, and 2 controllers, hotkeys work on one of the 2 controllers (in gamecube/wii) and you can exit with one of the 2 controllers
I believe the main issue is that:
only controller 1 in recalbox can use the hotkeys in all games/emulators at least on the PC version.
4 controllers plugged in and configures only controller 1 can use hotkey on all emulators.
i think all 3 of these issues are related. I would start with fixing hotkeys capability to all controllers and see if that fixes everything else.