Okay, so I've been having problems getting quest markers to show up for my dungeons, and I think I finally might know why (currently my Skyrim is re-installing, so I don't really have any way to test).
How necessary is finalizing the NavMesh? I've never done this, and I'm wondering is this is what caused my game to not place Map markers.
What do you guys think?

finalizing navmesh is absolutely critical, but i don't know if it's related to your issue.

quest markers are determined by target ref aliases.

I'm just thinking that without finalizing the NavMesh maybe the game doesn't know how to get from point a to point b. Maybe I'm just forlornly hoping, because my mod has the ref aliases in place and still won't place quest markers.