Does Godot support isometric multi-layering? I am making a isometric game with concepts of mountains and valleys that the rolling entities can pathfind around.

The blue entity can move from the ground layer to the next layer (the one encircled in red). I could fix this by cutting its navmesh around its corners (the one encircled in blue). This however is too much as I have do define duplicate tiles and give each duplicate a separate and unique navmesh.
How would one create an isometric map with multiple layers and on those layers, there is proper collision if the entity is on the same layer or 2 layers above, and if the entity is one layer above, it can path on its navmesh. It will not sense the collision if its one layer above.