This might be more complicated than expected. I have read something about autoconfig, but I think it doesn´t fit this case.
So, right now I am trying Plan B which is made a .cfg file for each 3 button game to override retroarch.cfg and have a 3 button game config.
Now the hard part of this is to find a list with all the 3 button games, or at least to able to filter down my roms to know which ones are "3 button game"
but so far I haven´t been able to find a list or find a method to filter down my romset.
Just the museum arcade have an advanced search with 3 button layout option, but it only show me 150 results .