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?