### 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)
const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	if (!tile_set.is_valid()) {
		return HashMap<Vector2i, TileSet::TerrainsPattern>();
	}
	
	RBSet<TerrainConstraint> constraints = p_constraints;
	
	HashMap<Vector2i, TileSet::TerrainsPattern> output;
	
	for (int i = 0; i < p_to_replace.size(); i++) {
		const Vector2i &coords = p_to_replace[i];
		
		TileSet::TerrainsPattern current_pattern = TileSet::TerrainsPattern(*tile_set, p_terrain_set);
		TileMapCell cell = get_cell(coords);
		if (cell.source_id != TileSet::INVALID_SOURCE) {
			TileSetSource *source = *tile_set->get_source(cell.source_id);
			TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
			if (atlas_source) {