I think it's just an oversight that RGUI doesn't have user # labels in the remapping interface. I have not done any work with the RetroArch UIs and I'm pretty backlogged with mame2003-plus coding. If no one has addressed this in a few weeks a month or two I will be more tempted myself.
I did start an issue here requesting it: https://github.com/libretro/RetroArch/issues/6843
It's probably not hard to add a new row that just says something like "User 1 Controls----" between each section but then again, maybe it is hard. :shrug: