I've also discovered more info, this ONLY occurs when playing the game with a controller

I would like to add to this thread by stating the Navigator seat entry point is completely erased on the unarmed version on the door. Now you must enter a pilot or passenger seat to then enter the navigator seat

Ive uncovered more detailed information. It turns out, the bug is instant as soon as the command wheel is opened. You dont even have to use it, the second it pops up, you will have to reload the world to unbreak it

They've never been functional. Its not a bug, its just designed that way

Also the reason the gamemaster bug is an issue is because the only fix is to reload the save/leave and rejoin