### 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)
max_size = kv.key;
			max_count = kv.value;
		}
	}
	set_tile_size(max_size);
	
	for (const KeyValue<int, CompatibilityTileData *> &E : compatibility_data) {
		memdelete(E.value);
	}
	compatibility_data = HashMap<int, CompatibilityTileData *>();
}
Array TileSet::compatibility_tilemap_map(int p_tile_id, Vector2i p_coords, bool p_flip_h, bool p_flip_v, bool p_transpose) {
	Array cannot_convert_array;
	cannot_convert_array.push_back(TileSet::INVALID_SOURCE);
	cannot_convert_array.push_back(TileSetAtlasSource::INVALID_ATLAS_COORDS);
	cannot_convert_array.push_back(TileSetAtlasSource::INVALID_TILE_ALTERNATIVE);
	if (!compatibility_tilemap_mapping.has(p_tile_id)) {
		return cannot_convert_array;
	}
	int tile_mode = compatibility_tilemap_mapping_tile_modes[p_tile_id];
	switch (tile_mode) {
		case COMPATIBILITY_TILE_MODE_SINGLE_TILE: {
			Array a;
			a.push_back(p_flip_h);
			a.push_back(p_flip_v);
			a.push_back(p_transpose);
			return compatibility_tilemap_mapping[p_tile_id][a];
		}
		case COMPATIBILITY_TILE_MODE_AUTO_TILE:
			return cannot_convert_array;