Just a quick update:
I tested csd’s suggestion and uninstalled the CMC extension (but left the Yamaha USB driver obviously) and the generic remote template loaded fine after a restart. Seeing the logic behind Shinta215’s hypothesis, I think it’s fair to say that indeed is the cause of the issue.
Now that Shinta215 and csd have done most of the work for them, I hope Steinberg will take it from here. 
Also, just for giggles I added 50 or so generic remote devices and in the last one I loaded my template for the CMC AI. I was hoping this would give enough time in between the CMC extension handshake and my generic remote device handshake, but alas…I didn’t think it’d actually work, but it was worth a shot. 