This may be long.
When Link is in mid-air (using the Roc's Feather) he can still go through the dungeon doorways.
Link should not go through the dungeon wall while mid-air until he lands, then he can go through as long there is no solidity (freeform dungeons rule)
But... but... what if there is no doorway?
Basically, this is a symptom of the current combo types vs. Roc's Feather.
This is a complicated bug................ You see Link, while in midair, if his shadow touches the bombed wall, he will keep the altitude as this door pulls him through. Same goes with the walk-thru.
Just do the Doorways: Locked, Bombable (already blown), Walk-thru, and Passage.
Link not to unlock the locked door with key in midair.
Link not to go through the passage (unlocked), blown, or walk-thru in mid-air.
What if you do a "jump over gap to reach the next screen"? I recommend you add checkboxes beside the door button in the Doors Dialog box that functions to prevent Link going through the dungeon wall in midair whether there is solidity (red mark) or not. If disabled, Link can go through while mid-air as long there is no solidity. (I don't know if my idea could make it...)
Again, this is a tough bug. All the developers should have to work together.............. and that quest rule: "Freeform Dungeons," I don't know.
Like L pointed out, this change would be complicated enough that it should be a full feature request, ie, not under consideration at this time.