After learning that booleans were apparently "bad" in my past question of this same problem, I decided to learn to use the knife tool instead to cut windows and doors in my ship.
Old thread: Blender exported mesh extremely deformed
Unfortunately, despite using the knife tool and everything looking allright in Blender, when exporting to fbx and using in ClothingToolCHECKED of the Nvidia apex cloth simulation, the cut outs were extremely deformed. This is the second time this has happened, even though I'm not using booleans!
This is very frustrating, as it took me a long time to redo the parts of my ship that had booleans in them.
Here are images of what I mean: