### 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)
TileMap *tilemap = Object::cast_to<TileMap>(p_node);
	if (tilemap == nullptr) {
		return;
	}
	NavigationPolygon::ParsedGeometryType parsed_geometry_type = p_navigation_mesh->get_parsed_geometry_type();
	uint32_t parsed_collision_mask = p_navigation_mesh->get_parsed_collision_mask();
	if (tilemap->get_layers_count() <= 0) {
		return;
	}
	int tilemap_layer = 0; 
	Ref<TileSet> tile_set = tilemap->get_tileset();
	if (!tile_set.is_valid()) {
		return;
	}
	int physics_layers_count = tile_set->get_physics_layers_count();
	int navigation_layers_count = tile_set->get_navigation_layers_count();
	if (physics_layers_count <= 0 && navigation_layers_count <= 0) {
		return;
	}
	const Transform2D tilemap_xform = p_source_geometry_data->root_node_transform * tilemap->get_global_transform();
	TypedArray<Vector2i> used_cells = tilemap->get_used_cells(tilemap_layer);
	for (int used_cell_index = 0; used_cell_index < used_cells.size(); used_cell_index++) {
		const Vector2i &cell = used_cells[used_cell_index];
		const TileData *tile_data = tilemap->get_cell_tile_data(tilemap_layer, cell, false);
		if (tile_data == nullptr) {
			continue;