Yeah that the fault of pathing, the engine wont attempt to path to occupied tiles, since that part also keeps unit from trying to walk into terrain. So if you block all your doors/lifts the engine treats it like a wall off. Unless someone want to rework the pathing code from scratch, doors with troops behind them are always gonna be like that.
The morale degen is supposed to partly address the need to get out of the craft and get to it. But it cant be much more severe then it already is, or you would panic way to much while hunting for the last few dudes in certain maps/missions.
One could put the self destruct charges from the supply ship on more faction vessels, but that may not be appropriate for a blanket use.
