The easiet way to get the games to run with Launchbox would be to strip the command line of the path to retroarch,exe and the core part.
e.g.
atom -rompath “H:\LaunchBox\Games\Acorn Atom” -flop1 “H:\LaunchBox\Games\Acorn Atom\atom\galxians.zip” -autoboot_delay “2” -autoboot_command “ *dos\n* dir\n *cat\n* run"galaxi”\n”
…put that in a galaxians.cmd and load it like a rom.
Like I said… I have gotten this to work on a couple of systems but it breaks weirdly
on others. I think it is worth a shot for you to try though.
This is a problem unless you are OK with disabling software lists in the opt. (If you are never going to use the traditional method.
There are times when you actually need the traditional method (FM-Towns that need a boot disk.)
I have yet to find a way to use a boot disk and iso/chd in the command line.