In Dungeon Builder, after you link a corridor to a room you can drag the handle up along the wall so it isn't linked at floor level. They way you do it is to select the toolbar button that has the red horizontal line (the one that looks like the red bar you see at all intersections). When you select this, all intersections will show a square handle at the floor of the connecting corridor. Then you can move the corridor up the wall of the room by holding <Shift> down and dragging the handle up (holding down the Shift key lets you drag handles up along the Z axis, but I figure you already know this).
The rest are great points and when I get some time I'll see what I can implement. I also took a look at your other post about the OpenZone bug, but I couldn't open your link to the 3ds file to test it. It was telling me the file isn't there.
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