I think RetroArch doesn't care about extensions...
Jeezy Creezy.... It was just that easy.
Ahhhhhhh well. At least when I'm wasting a ton of time and the answer is just this simple at least I'm learning new things, right?
I absolutely can't believe the best answer was changing .bin to .cue. Works perfect for launching the game, and it shouldn't give any problems with our script either.
Thanks everybody!