We all need a break, I'm taking one right now
It's possible DFU only looks at certain models for door detection, been a while since I looked at it but I know the detection occurs when DFU rebuilds the Daggerfall model data to a mesh that Unity can use.
I also know Azimov ran into that issue when he was working on that custom exterior / interior, I think it was for this mod:
https://www.nexusmods.com/daggerfallunity/mods/234. He used the loose wall pieces to build a bigger exterior building but then it wouldn't work.
If you do want to be able to work with the wall pieces, you could just make the mesh yourself and then use the RuntimeMaterials script in Unity to assign vanilla textures making it replacer compatible at the same time and also add one or more CustomDoor components to define your doors. I think that may be the road with the least headaches.
Alternatively, you could post the JSON or model IDs that aren't working, I'm not sure if Interkarma intended to cover all models with doors or just the actual buildings. The interior / exterior doors in Daggerfall aren't linked, DFU just picks the door that's closest position wise, it works because of how the interiors kind of correspond to the exterior shape. I'm not sure how it would handle stuff that's added on though since the exterior building is meant to be one object.