Somewhat solved.
I went back into Bluetooth and removed the XBox controller from the paired listing, and then added it back in the usual way, and this time got no error (maybe due to the XPadNeo being installed ?), and then did the Input configuration again, and now the Middle Button + X brings up the menu to quit the games etc, like the Pi3B+ did.

Its super weird as I re-did the Input configuration 3 times and that did not solve it, before I tried removing the controller completely and adding it in again.

There certainly seems to be some sort of issue here, but I am unsure what it is exactly.

@dankcushions said in Commands to quit frozen/bad roms? (not Ctrl + C or F4):

so the thing to note here is lr-mame is in the 'experimental' section of the retropie package manager. experiments fail :P

It wouldn't be an experiment if we knew what was going to happen :)

lr-mame2003-plus seems very reliable for me, with helpful features over lr-mame2003. Is there a list of remaining issues, or a process for that to go through before it becomes a regular optional or main package?

@MrStruders If by fresh install you mean using a new image, then no, since the new image will write everything from scratch. Can you run another update, also updating the OS and packages when prompted, of the RetroPie-Setup script ?