### 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 (p_atlas_coords.x < 0 || p_atlas_coords.y < 0) {
		return false;
	}
	if (p_size.x <= 0 || p_size.y <= 0) {
		return false;
	}
	if (p_frames_count <= 0) {
		return false;
	}
	Size2i atlas_grid_size = get_atlas_grid_size();
	for (int frame = 0; frame < p_frames_count; frame++) {
		Vector2i frame_coords = p_atlas_coords + (p_size + p_animation_separation) * ((p_animation_columns > 0) ? Vector2i(frame % p_animation_columns, frame / p_animation_columns) : Vector2i(frame, 0));
		for (int x = 0; x < p_size.x; x++) {
			for (int y = 0; y < p_size.y; y++) {
				Vector2i coords = frame_coords + Vector2i(x, y);
				if (_coords_mapping_cache.has(coords) && _coords_mapping_cache[coords] != p_ignored_tile) {
					return false;
				}
				if (coords.x >= atlas_grid_size.x || coords.y >= atlas_grid_size.y) {
					return false;
				}
			}
		}
	}
	return true;
}
bool TileSetAtlasSource::has_tiles_outside_texture() const {