This mod makes changes to Atrium Doorway Bottom, the Atrium Doorway Top, and each of the room doorway pieces, but not the room corner doorway picees.  The changes it makes include 

 * In the editor dialog it changes the NavMesh Generation Import Option value from Collision Geometry to Bounding Box.
 * For the Atrium Doorway Top piece only, it removes the navmesh on the roof of the piece.

This was the minimal set of changes I found would work to allow NPCs to traverse those pieces.

To be honest, these changes are an imperfect work-around for a bug in the dynamic navmesh building code in the game engine.  Collision Geometry is the more sensible option for navmesh generation, it just doesn't work in these cases.  Bounding box makes the entire workshop piece appear traversable to an NPC.  This means they sometimes bump into the sides of doorways since they think they can walk through them.  It's not perfect, but it's the best I could do.