Nope.
Gives me an idea though. I use AttractMode for my front-end (which runs outside of X). The layout system of AM is very flexible, and it has a pretty robust set of tools for reading and writing files. For instance, I recently wrote a module for it that parses MAME layouts files and displays the bezels and such with the AM layout. I also have a module that relatively positions content within the AM layout. I could probably use some of the code I used for the MAME artwork along with the positioning module to generate a configurable controls overlay.
That said... I can't remember if ADVMame uses readable controller cfg files or not. I was thinking that last time I tried to open them it was gibberish that I couldn't easily parse. Reading the Pi's controller configuration files is pretty simple, but not sure about ADVMame. It would be easy to read controls.ini files too.
Anyway, the answer is still "Nope." But making the answer "yep" instead sounds like fun. Short term, there's not a good option on the Pi that I'm aware of.