From what I understand, each TileMap node can only be on one layer, so I made bottom, middle, and top layer TileMap nodes for different kinds of tiles. But if I do something like put a tree trunk on the middle layer and the tree top on the top layer, the player can go behind and in front of the tree (which is good), but he can also stick his feet through the tree (from above), or stick his body between the top and middle layer tiles. He's some pics of what I mean: good, good, bad, bad
Normally I guess I would put StaticBody2D nodes to block the top of the bottom tile and bottom of the top tile, but then that would break the Navigation, because I have to either have an entire tile be a NavPolyInstance or have no NavPolyInstance but a StaticBody2D instead.
Anyone else having issues with multi-tile trees/objects on TileMaps that have NavigationPolygonInstances in them?