I think I resolved this, but will follow up shortly to confirm.
I removed all of the pre-installed controller .cfg files from the RetroArch directory and re-ran the configuration utility. After that was completed everything seems to be working fine, my “Y” button is now mapping as the “A” button in Genesis as it should.
It appears that maybe RetroArch was loading up a different .cfg file for my controller rather than the one that was created specifically for it.
I’m going to try SNES and confirm.