While looking at the CK for sources of my CTDs in cell -2,2 I looked at some neighboring cells.
Vanilla cell -1,1 has a duplicate navmesh laying on top of the regular navmesh. You can't see this unless you select a cell, and delete it. There is an exact copy right below it throughout the entire cell! (Don't save that CK session if you delete a cell - it would be a dirty edit and unpredictable; just exit w/o save!!)
What effect on the game might that have?