@Concat, @BuZz
I really appreciate the extras eyes on this to confirm what I was seeing. I can't reproduce the problem on Windows or the MacOS, so maybe it's a Linux-specific issue. I'll open a ticket and see what the RetroArch team has to say. Thanks BuZz, for searching the sourcecode. I need to learn how to do that somewhere down the road. Also, thank you Concat for the map testing. I was beginning to think I was imagining the whole thing ;).
In an effort to move forward with my own goal, I'll have to rethink and even compromise the idea of a universal gamepad control scheme for now, but I have a few ideas in mind to easily allow switching between control schemes for all the systems that currently lack Joystick support. Perhaps a series of script templates that can easily be installed and launched from a sub-directory in the 'RetroPie' menu in Emulation Station. This might be better in the long run as the end user could duplicate and configure the templates on a game-by-game basis for systems like the ColecoVision that need a more refined control scheme depending on the game.
Edit: Also, thanks for the last suggestion Concat. While it doesn't meet the global requirements I need, I'm definitely going to keep that trick in mind for the future.