Ysort and stuff related has become so much easier with the Layers in 4.
I just stumbled on this, looking up Godot content.
For other stumblers:
in Godot 4.2, you can make Layers to a TileMap, name them anything like Ground, Cliff, ysort... and make ysort assets on the ysort layer.
So, Ground[LV1] can be like floor tiles, small plants, anything you can walk over.
No worry on collision layers, just floor art.
Cliff/Wall [LV2] can be anything you want to put a collision on, like a wall or cliff. Example, you can't walk up a cliff, so make a collision on cliff or wall tiles. But, you want to be able to be able to walk on top a cliff area/behind a wall, so just collision on that layer of the proper tiles.
ysort [LV3] is where it gets fun/complicated:
You put any tile assets, that you want ysorting on, in this layer.
Grass, flowers, floor, stays on LV1.
Lv2: Front facing Cliffs, front facing walls, you give a collision shape, and only them.
Lv3:
Trees, crates, backside of cliffs/walls, ect, you single out those assets, add a Physics layer, collision, Ysort origin, on those.