### 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 (polygon_index >= physics[layer_index].polygons.size()) {
					physics.write[layer_index].polygons.resize(polygon_index + 1);
				}
			}
			if (components[2] == "points") {
				Vector<Vector2> polygon = p_value;
				set_collision_polygon_points(layer_index, polygon_index, polygon);
				return true;
			} else if (components[2] == "one_way") {
				set_collision_polygon_one_way(layer_index, polygon_index, p_value);
				return true;
			} else if (components[2] == "one_way_margin") {
				set_collision_polygon_one_way_margin(layer_index, polygon_index, p_value);
				return true;
			}
		}
	} else if (components.size() == 2 && components[0].begins_with("navigation_layer_") && components[0].trim_prefix("navigation_layer_").is_valid_int()) {
		
		int layer_index = components[0].trim_prefix("navigation_layer_").to_int();
		ERR_FAIL_COND_V(layer_index < 0, false);
		if (components[1] == "polygon") {
			Ref<NavigationPolygon> polygon = p_value;
			if (layer_index >= navigation.size()) {
				if (tile_set) {
					return false;
				} else {
					navigation.resize(layer_index + 1);
				}
			}