They can't be opened from the bottom side after a stack of passthrough parts, because there's no rail collider to switch your current part to the docking port.

They allow passage out of the ship and/or into unsupported parts.

Possible solutions:
-make the top-side hatch understand that it should not open when the bottom isn’t connected to something valid
-swap these out for real hatches
-make a version of the invisible hatch that has a collider and depth mask, so you just see the exterior of the attached part