I don't understand how priming both extruders would help? The unused or sparsely used hotend would still burn the filament if that's causing your restart issues. If designing the dual extruded object, use the unused hotend to make up the infill to keep the filament flowing. Sorry if I don't understand the "restart issues" quite fully.
As for discoloration of the second filament after a long layer, it should be caught on the prime tower? If not, try using the ooze shield in conjunction with the prime tower. If the ooze shield ends up "leaning" and interfering with the print, try a second outline to act as support for the shield.
Adding a feature to cool/heat unused hotend would be interesting. But sounds difficult to implement properly for every machine type. Ensuring the hotend gets up to the right temp would be challenging. Brainstorming.... a secondary "cooling" temp could be implemented, then a reverse "coast" could be used to time when to heat back up. I guess a "pause" could help with heating... but I'd prefer to have a continuous print.
Currently, I either manually shut down the unused hotend or "program" the temps into the process... or use multiple processes. Would be nice to have it automated, but I'm not holding my breath.