Update: Apparently there is a check cover edges button which needs to be pressed before pressing finalize in all cells affected. So as long as you have no warnings, and have your nodes z axis lined up close with your triangle edges touching each other. This will most of the time create a new green line for you (apparently it is called a cell boundary line) and not having means npc's will not cross from one cell boundary to the next without that green line even if the navmesh triangles are touching.
I have found you can occasionally create this line where no boundary was before using only finalize, but this doesn't seem to be the case when you delete them or make edits that remove the green line. At least for me. So hope that helps if anyone else comes here wondering. This is still very much a pain as the vanilla cell boundaries tend to mess up easily when you edit anything near them. And sometimes your finalize navmesh seems to become undone when you save sometimes
Edited by kingbeast88, 18 January 2018 - 11:22 PM.