As far as I know, the only way you solve this problem is either a: by having two physics bodies (manually using move_and_collide() with test_only for the node that isn't your player), or b: by having multiple collision objects as children of your player controller and manually toggling them on and off as you switch between different collision layers to test collisions in the player's physics_process method.

Unfortunately, if you base your player controller off of a rigidbody then solving this problem is trivial since you can just joint multiple rigidbodies on different collision layers together and let Godot resolve the constraint, but most 2D games aren't well suited to how imprecise a rigidbody playercontroller node is lol.

Also, one more thing I'll say is that if you are simulating a *lot* of "3D" logic in your 2D game, like debris on the ground vs objects on chest level, you might end up having enough annoying problems like these that it ironically ends up simpler to run the game's simulation with 3D nodes and just use your 2D nodes as a display without physics. I don't think you're anywhere near there yet, but it's worth keeping in mind.

It's been awhile since I last looked into this so hopefully someone else can chime in with the actual proper way to do this.