Well, it's fine to leave the same reference ID, but I think it's unnecessary, unless you know that particular reference is already part of a quest or something.
Actually, it turns out to be needed for a number of reasons.
1) mods that overlap. If 2 mods change the same doorway (the problem I was trying to solve), they need to replace the base reference (not edit the base object as I incorrectly made this subject), but keeping the same object ref. Otherwise, you have overlapping scenery.
2) NavMesh. There are Crashing To Desktop problems with deleted or replaced NavMesh, so you have to maintain the same object ref, as it's also a reference inside the NavMesh itself.
3) as you mentioned, scripted object references, although not my problem here.
Again, I thank folks for helping me with this issue.