I got it working, basically. inputFolder=, et al, were the answer.
.skyscraper/config.ini:
# ...
[pcengine]
# use "tg16" folders for pce/tg16 titles
inputFolder="/home/pi/RetroPie/roms/tg16"
gameListFolder="/home/pi/.emulationstation/gamelists/tg16"
mediaFolder="/home/pi/.emulationstation/downloaded_media/tg16"
cacheFolder="/home/pi/.skyscraper/cache/tg16"
# importFolder="/home/pi/.skyscraper/import/tg16"
# ...
Then I moved everything around in my filesystem to match these changes.
This allowed me to point .emulationstation/es_systems.cfg at the roms/tg16 folder and still have the gamelists display correctly in ES. I did have to clear out the tg16 videos from my media folder (symlinked to ones in cache/pcengine that no longer exist) and build the gamelist one more time to fix the links but after that, it works fine!
cacheFolder and importFolder don't really affect the gamelist end result, I just included them so that if a proper tg16 platform ever is added, everything will already be in the right place. (Edit: Setting importFolder gave me an error that the path does not exist when I tried to --cache edit on a rom. Even though it doesn't exist for any of the other systems either, but since this one is defined specifically I guess it really wants it to exist. Commenting out that line eliminated the error.)
There was one more hitch. The runcommand launch art doesn't use the <image> file defined in the gamelist, but rather looks for a file matching the rom's name, in a folder matching the system name called by the run command (in es_systems.cfg). The original solution, that I had done with Genesis/Megadrive, was just to symlink the media folder to one matching the run command named system. But in the interest of completeness, I now decided to go the other route and just change the run command to call the proper system instead. So I changed _SYS_ pcengine to _SYS_ tg16 and then all I had to do was copy the /opt/retropie/configs/pcengine folder to tg16 (symlinked, so as not to duplicate data unnecessarily. I could have just renamed them, but keeping the links intact for the config and rom folders, allows me to retain the dual nature of the systems, while simultaneously keeping it hidden beneath the surface.)
Now I guess the only problem is it works so well on the surface, I keep forgetting and trying to use -p tg16 by accident :-S
Edit: well there was a little more under the hood work involved in getting the system(s) fully switched over. Both emulators.cfg and retroarch.cfg reference a system folder, so I scrapped the symlinks and just renamed the config folders, then replaced all instances of "megadrive" or "pcengine" with "genesis" and "tg16" in those files. Bonus: I learned about the sed command:
sed 's/<old_text>/<new_text>/g' <file>
e.g.
sed 's/\/pcengine\//\/tg16\//g' emulators.cfg
...prints the result to stdout. (I wanted to match the string /pcengine/ and not just pcengine just in case it was in an emulator's name or something. It looks like they all just said "pce" but it doesn't hurt to make sure.)
You can pipe it to an output file with > <file> e.g.
sed 's/\/pcengine\//\/tg16\//g' emulators.cfg > emulators.cfg.new
...or
sed -i 's/\/pcengine\//\/tg16\//g' emulators.cfg
...modifies the original file with -i or --in-place.
