RetroPie just packages RetroArch - you may want to report to the upstream project. You should add a way to reproduce the issue without relying on a specific device, so that any developer familiar with RetroArch's input system may be able to analyze and maybe fix your issue.

Sorry, no idea.

By the way the LEFT and RIGHT buttons on my remote work by default so I am hoping there is some way I can utilize the current functional implementation rather than hacking up something in python. Any clues?

Related posts here and here.