It seems unlikely to be able to just walk up to an alien ship and know how to operate their doors. Have 2 ways to open ship doors. One would be explosives, in which case the doors open perminantely. Second would be researching a technology to operate/activate some alien devices/technology (perhaps would apply to more than doors), in which case you could operate them freely. Can open and close them manually at will. To get around the AI struggling with players opening the door, shooting through the door, then closing it, simply give the AI remote control to the doors. Maybe they have remotes on their arms, or panels in the ship that can remotely operate their own doors. Bottom line is regardless of distance from the door, once the AI is aware of players outside the ship they can open/close the doors at will from a distance.