@reroshaggy I still think that you're trying to make things way too much complicated, but that's your problem afterall đŸ˜‰
Regarding your questions :
is there an option to have a controller config, specific to my controller(s) that I can set up with mappings?
I'm not sure I understand
How does the emulator knkw which controller to allow hotkey button usage
Easy : only P1 HK is configured. And for all emulators but N64, we can decide the controllers order