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!