While researching I stumbled over these lines in the Skeleton config:

# Input device buttons. # Figure these out by using RetroArch-Phoenix or retroarch-joyconfig. # You can use joypad hats with hnxx, where n is the hat, and xx is a string representing direction. # E.g. "h0up"

But where do I find these 2?
Both just returned me a command not found error.

RetroArch-Phoenix and retroarch-joyconfig

Also I don't have enough buttons to go through the auto config tool, so that simply is not an option. At least it seems so since I could not find a way to skip buttons or end it before going through all of it.

Tried the obvious things like using a keyboard:
press esc
press tab (to select the exit button)
press arrow keys (to select exit button)
press enter, well just for good measure at this point

Logging into ssh to check if it maybe already saves progress mid way through:

ls /opt/retropie/configs/all/retroarch-joypads Microsoft X-Box 360 pad.cfg Microsoft X-Box 360 pad.cfg.bak

Well, that seems like a no, so I can't just shutdown now and just fix up the file manually later with the intel obtained from the partially configured one.

I'm going to try with rejoystick (http://rejoystick.sourceforge.net/)

Do we know it?

@yfzdude great many thanks

I did some further testing for some new translations that I patched and I have to do a bit of embarrassing back-pedaling here. I'm not too proud to admit when I made a mistake. :)

L1 in lr-nestopia does "everything" in the RetroPie. It will flip the disk and load it, and it won't do this when you're not being prompted to flip it, so there is no danger that it will screw up your game. I will resume testing on FDS for now, but there has been 1 rom out of about 6 or 7 that I've tested so far that boots back to the romlist in lr-nestopia, so that leaves us with lr-fceumm's completely different system for loading. I'm assuming there is nothing that can be done to fix lr-fceumm to behave like lr-nestopia since the XBox version of NestopiaX has a similer "flip disk" command in the menu that behaves identically to pressing L1 on the pad in RetroPie. (Actually, this is one instance where I prefer how RetroPie handles things).

There still is the issue of hotkey mapping though. There doesn't seem to be any good way of doing this on a per-system basis that works. Is the information on the github in the following link bad now?

https://retropie.github.io/RetroPie-Docs/RetroArch-Configuration/#example-per-system-control-override-retroarchcfg