I use RA for every system, except for MAME. I got curious as you said that MAME RA core runs better than standalone. Maybe its time for me to move on to the MAME core.
Love the idea of porting your creations to RA and the fact that the screen position and X/Y are saved per game, the configuration of your bezels will be seamless. Thanks for your hard work Orion
For the multiple core thingy, I feel your pain; there is now a way of saving configuration per folder, so even if two systems use the same core, you can differenciate their settings in that way (if the roms are placed in different folders). When I configured my RA stuff some years ago, that was not implemented so I had to copy and rename the core, and copy and rename its info file, to emulate like a second different core.
About the key configuration; have you tried the “Save Core Remap File” or “Save Game Remap File”?