@RandoCalrisian It's pretty impressive how fast you moved through this problem to a solution. The community here is great!

I do agree regarding the emphasis on the hand-held controller method of defining inputs. My cocktail setup sounds similar to yours--three panel, vertical games played from the ends. Because most of the console emulators are horizontal, my default retroarch.cfg is setup with that in mind, but I have a lot of in game adjustments in lr-mame2003 GUI. For FBA my default mapping is a NeoGeo setup, yet that forces me to do per-rom configs for most fighter games. You are definitely doing the right thing, or rather, the necessary thing to get what you need. It's tricky, but I appreciate how flexible it is. The biggest win from my perspective with RetroArch is the shaders. It's so great to have passably realistic scanlines and curvature across multiple systems. The exception for me is vector arcade games which I use AdvanceMAME exclusively for it's ability to specify high resolution.