I'm not sure if you fully caught what I was suggesting...
But I also didn't think it through thoroughly, so it may be a moot point.
... Or maybe not...
What I was thinking was, where you would normally put the trap door NPC, you put an event trigger instead (fight with trap door). Then, assuming victory, the tile just beyond that would be the warp point. You could use the same event call for every instance of this, except the trap door would re-arm every time.
This wouldn't be a huge problem, though in theory...
Ok, here's what I'm thinking:
Let's say there's normally a trap door NPC at coordinates 15,5.
That means that the door is also at 15,5.
You'd have to make sure the door for this tileset is a trigger (I'm not looking, so I don't know). The trigger built into the door would be the event call for the trap door fight (that would be the only component of the event).
Then, at 15,4 there would be another trigger point that would function as the warp to the next room. In the next room, instead of a "return" tile, you'd have a warp tile to exit. This warp would warp you to 15,6 so that you don't have to fight the same trap door again if you don't want to (but it would be there again if you did choose to reenter that room).
In theory, this would all work. You'd have to eliminate practically all return tiles in the dungeon because of stack issues this would cause otherwise. Some players might object to regenerating trap doors, but it would be consistent with the challenge level of Combat Boost, and a second fight with each would be entirely elective. By doing it this way, you could reuse the same event call for every trap door.
Does that make sense? Sorry, I was kind of thinking it out as I typed... But I think it would work.