I also couldn't make this working. Everywhere I ask and all respond the same way that it works by doing the same as for regular square tilemaps. It works for a square tilemap, but not on an isometric tilemap.
I believe it is either the case that I don't know the workflow or it is a bug.
I am talking about the auto-navpath.
One workaround is, not to do auto-navigation, instead put the navpath as a sibling of the tilemap and do all adjustments manually.