As per the title, I think it would be super useful to be able to spawn prefabs with prefab navmeshes and NOT have them snap to the closest grid position, but rather make their own graph which can then be connected using links. In my use case I dynamically spawn apartments in buildings, there are many buildings with different positions (and rotations!) that can almost never snap to the tiles.
BTW, loading+unloading Navmesh Prefabs still leaves the tiles in a broken state, as mentioned in the other topic: 5.1.3 - Navmesh Prefabs offset + odd tiles