I'm mostly working with old handhelds. The Arcadia 2001 is an exception.
The other systems would be the Hartung Game Master, the Watara Supervision, Milton-Bradley Microvision, and the Creatronic Megaduck.

As far as test games I am using the following:
Arcadia 2001: Astro Invaders
Hartung Game Master: Continental Galaxy, Space Castle
Watara Supervision: Jaguar Bomber
Creatronic Megaduck: Pile Wonder
Milton-Bradley Microvision: All of them.

All seem to work in my desktop version of Mame 0.180, but somehow lr-mess-2016 doesn't like them. Everything seems to be in order with required BIOSes for the Game Master.

I looked in the ini files and found preferred names for software (e.g. Continental Galaxy 2020 becomes cg2020 and retitled the .bin files and .zip files accordingly, but still nothing.

I recently tried running Space Castle on Game Master again, and got this in runcommand.log:

Executing: /opt/retropie/emulators/retroarch/bin/retroarch -L /opt/retropie/libretrocores/lr-mess2016/mess2016_libretro.so --config /opt/retropie/configs/gmaster/retroarch.cfg "/home/pi/RetroPie/roms/gmaster/scastle.zip" --appendconfig /dev/shm/retroarch.cfg

"scastle" approximately matches the following
supported software items (best match first):

/opt/retropie/supplementary/runcommand/runcommand.sh: line 961: 917 Segmentation fault /opt/retropie/emulators/retroarch/bin/retroarch -L /opt/retropie/libretrocores/lr-mess2016/mess2016_libretro.so --config /opt/retropie/configs/gmaster/retroarch.cfg "/home/pi/RetroPie/roms/gmaster/scastle.zip" --appendconfig /dev/shm/retroarch.cfg

UPDATE: I am currently trying these games on the desktop version of MAME 0.174 instead of MAME 0.180, as lr-mess2016 is apprently based on MAME 0.174. Desktop MAME 0.174 64-bit is running the Supervision and Game Master games just fine. Megaduck test game works in Desktop MAME 0.174 as well, though apparently I had the alternate version of Pile Wonder.

UPDATE: Game Master, Megaduck and Supervision games match names and CRC hashes with the games listed in the XML for lr-mess2016 and Desktop MAME 0.174. However, so do 13 of my 15 Microvision games, which don't appear to work in Desktop MAME 0.174 or lr-mess2016. Weird.