### 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)
if (components[1] == "collision_layer") {
			r_ret = get_physics_layer_collision_layer(index);
			return true;
		} else if (components[1] == "collision_mask") {
			r_ret = get_physics_layer_collision_mask(index);
			return true;
		} else if (components[1] == "physics_material") {
			r_ret = get_physics_layer_physics_material(index);
			return true;
		}
	} else if (components.size() >= 2 && components[0].begins_with("terrain_set_") && components[0].trim_prefix("terrain_set_").is_valid_int()) {
		
		int terrain_set_index = components[0].trim_prefix("terrain_set_").to_int();
		if (terrain_set_index < 0 || terrain_set_index >= terrain_sets.size()) {
			return false;
		}
		if (components[1] == "mode") {
			r_ret = get_terrain_set_mode(terrain_set_index);
			return true;
		} else if (components.size() >= 3 && components[1].begins_with("terrain_") && components[1].trim_prefix("terrain_").is_valid_int()) {
			int terrain_index = components[1].trim_prefix("terrain_").to_int();
			if (terrain_index < 0 || terrain_index >= terrain_sets[terrain_set_index].terrains.size()) {
				return false;
			}
			if (components[2] == "name") {
				r_ret = get_terrain_name(terrain_set_index, terrain_index);
				return true;
			} else if (components[2] == "color") {
				r_ret = get_terrain_color(terrain_set_index, terrain_index);
				return true;