@simpleethat thanks for the info. Yeah, they are both 16x9, 1080 is 1920x1080 and 720p is 1366x768. I think everything is set to 1920x1080 on my pi currently. Hoping to find out if I have to change any settings to step down to 1366x768 (720p) for proper framing?
@stoo Having lots of differences between FBNeo & MAME for system16 based hardware isn't surprising, system16 is a historical driver for Final Burn (first FB driver and first emulator to run that hardware, the emulator's name is actually based on "After Burner"), current FBNeo driver is built upon that initial driver. You should report the glitches at https://github.com/finalburnneo/FBNeo/issues, we can't fix what we don't know about :)
EDIT: OK, so I double-checked the md5s of the bios files that i have downloaded BEFORE and AFTER sending them to the pi (just in case they would get corrupted as they were sent or something) they matched on winmd5 just fine.
lr-pcsx-rearmed can use only scph5501.bin from the list of BIOS files you have, and that file has a wrong MD5 in your screenshot - it's not what's in the docs or what the core expects.
Unfortunately I can't get a copy of the game to test, but can you just get a RetroArch log file and put it on pastebin.com - enable Verbose logging in the Runcommand launch menu, run the game for a while, then upload the /dev/shm/runcommand.log log file to pastebin.com and paste the URL here.