With MCC, there's no interior temp sensor so AC temp is then controlled only by closing doors within the heater box, no heater control valve either and coolant always flows through the heater core.

As for your idea to bypass the heater core, you can do it if you want but IMO it's not necessary. If you're determined to do it, just re-route the hoses that that it's completely bypassed. I'd leave to core inside the car as there's no good reason to remove it.