You can't. You need to use the animated door prop that folds into itself rather than parenting a non-animated prop. Though the invisible func_door will still pass through the ceiling and be solid, so it hopefully will be clipped off.
make it open a different direction (down, left, or right) would be my suggestion. or place another piece of building in a clever way to cover it while still being aesthetically pleasing.
yeah. that's a pain in the butt. but the only solution that i've seen on maps that should have this problem is making it go down. but it looks kinda weird.
You could always just add a sign there, such as the Blue shipping or Red towing if you don't want to do the other things mentioned. This will allow you to block it quite fast, but might not work in other situations.
If this is your first time logging in after the migration (Feb 8, 2022), you must reset your password to log in. Follow this guide if you're having trouble