I forgot to mention this, but:
In the left image, you see that the passages (including those for bombed walls) and overheads for the left and right Out Lands Doors (circled in red) are fully walkable, because there are no red squares on the top half in the walk box. In the right image, the Z1 passages (including those for bombed walls) and overheads (circled in green) are walkable on the bottom half and un-walkable on the top half, because the top half of the walk box is filled in by red squares.
So, I had to edit the Out Lands Passages (including those for bombed walls) and Overheads (circled in blue) by clicking the top corners of the walk box, just to make the top half of those passages and overheads un-walkable, because if they're walkable, Link could end up stuck in the wall of a guy room (on the top half of the passage combo), unless the 'free form dungeons' rule is turned on.