Aha, I actually figured out how to make it work, for anyone reading this in the future!

The problem is for whatever reason the entry that emulationstation creates just starts with "roms/gbc." It works once you simply replace "roms/" with "./" in front of that, which is what is listed for the paths for games before the rom name too (and I suppose substitutes for the entire filepath to the root folder). So adding this to my sgb gamelist...

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Creates this in my emulationstation system for SGB:

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Which is exactly what I was hoping for. Clicking through those two directories takes me to all my SGB-compatible GB and GBC games, and I didn't need to add duplicate roms to do it as the gamelist points to the GB/GBC rom locations I have for those systems. Woohoo!

GameKing gamelist with videos and boxes is now available here

@mitu thank you as always! Will give this a go.

@IanDaemon that's exactly what I plan to use it for. All of the game sequels done with Roman Numerals can be displayed as the publishers intended but also in sequential order.

You're using a very old RetroPie version, is there are reason for you to do that ?
Regarding your issue - most likely EmulationStation cannot create any new files, since the filesystem is 97% in use. On Linux, by default, a filesystem will have 5% reserved to the root user to prevent users filling it accidentally (or maliciously).
Run EmulationStation manually, then exit (via the menu or F4). Check the log file in ~/.emulationstation/es_log.txt and see if any errors occur when exiting (like files not being able to be created, etc.).

Looks like it could be. I'm about to leave for work so I will test more tomorrow. But quick glances show it now has that whole path set up as pi:pi.