### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
Vector<String> components = String(p_name).split("/", true, 2);
	if (components.size() == 2 && components[0].begins_with("occlusion_layer_") && components[0].trim_prefix("occlusion_layer_").is_valid_int()) {
		
		int index = components[0].trim_prefix("occlusion_layer_").to_int();
		if (index < 0 || index >= occlusion_layers.size()) {
			return false;
		}
		if (components[1] == "light_mask") {
			r_ret = get_occlusion_layer_light_mask(index);
			return true;
		} else if (components[1] == "sdf_collision") {
			r_ret = get_occlusion_layer_sdf_collision(index);
			return true;
		}
	} else if (components.size() == 2 && components[0].begins_with("physics_layer_") && components[0].trim_prefix("physics_layer_").is_valid_int()) {
		
		int index = components[0].trim_prefix("physics_layer_").to_int();
		if (index < 0 || index >= physics_layers.size()) {
			return false;
		}