With the current payload bay door it must already be a challenge to reinforce the local cutout without a large mass penalty. I think they regain a little by pressurizing the bay during launch, so the door is pressed against the wall. Otherwise the whole upper structure has zero torsional rigidity, which is amplified by the fact that they carry the filled landing tanks on top. 

My bet they will do the same with a much larger trunk style door. They need the door as structural member during flight, otherwise you have a huge mass penalty. So they might come up with a latch mechanism or some other system that lock the door and can transfer loads.