It's not an idiotic problem. I thought I'd never do a custom area with doors because of this very issue. Open floorplans: that's the ticket!
It's only been this past summer working on areas for Surayah and the De'Arnise Romance that I managed to do some successfully.
This looks like the original building the door goes with is not in an identical position within the 64x64 blocks, so it won't insert seamlessly. What I do in this situation is open the bitmap of my area in Photoshop (Or any graphics program that will allow you to work wth layers and gives the cursor's x,y coordinates.) then add the closed door bitmap I extracted with IETME as another layer. I move and possibly do some erasing of edges of the closed door until I have the closed door aligned just right. Then, I merge the layers and save the area bitmap under a different name. Finally, I get the coordinates of the lower left-hand corner of the 64x64 grid block where the new door bitmap is going to align in IETME. In your case, it looks like you'd have to start your new closed door at (128, 192), then make it 192px wide and 256 px high to make sure the needed sections are covered, but still divisible by 64px. I then take those coordinates, go back to the closed door version of the area I did in Photoshop and cut and save the precise area I need to insert.
That's the general process for making your own closed door bitmap. It's the kind of thing I should make make screenshots of the next time I'm doing it and write a tutorial, because I think there was an additional tweak, like you need to start at [x-1, y-1] because the x-y intercept is at [0.0], otherwise it winds up just slightly off. Unfortunatey, I don't have access to modding tools right now, where I can double-check.