Two small one-room interior cells have bad or missing navmesh. They are RelayTowerInt17 (001B9A59), which is the basement in Shaw High School where the Super Mutant radio is being broadcast from, and RelayTowerInt12 (001DE7E3), which is the old but still accessible military bunker at the Fort Hagen Satellite Array (not the Rust Devil's HQ, but the original cell for the Array). Not having navmesh will keep any NPCs, including companions, from being able to use these cells.
I've published a patch that fixes this, and give permission for you to use it. It also created a RoomMarker automatically for RelayTowerInt12, which was missing. PPF has one as well.
My patch is located at
https://www.nexusmods.com/fallout4/mods/93783