### 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();
	Transform2D gl_transform = tile_map_node->get_global_transform();
	RID space = tile_map_node->get_world_2d()->get_space();
	PhysicsServer2D *ps = PhysicsServer2D::get_singleton();
	
	TileMapCell &c = r_cell_data.cell;
	TileSetSource *source;
	if (tile_set->has_source(c.source_id)) {
		source = *tile_set->get_source(c.source_id);
		if (source->has_tile(c.get_atlas_coords()) && source->has_alternative_tile(c.get_atlas_coords(), c.alternative_tile)) {
			TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
			if (atlas_source) {
				const TileData *tile_data;
				if (r_cell_data.runtime_tile_data_cache) {
					tile_data = r_cell_data.runtime_tile_data_cache;
				} else {
					tile_data = atlas_source->get_tile_data(c.get_atlas_coords(), c.alternative_tile);
				}
				
				for (uint32_t i = tile_set->get_physics_layers_count(); i < r_cell_data.bodies.size(); i++) {
					RID body = r_cell_data.bodies[i];
					if (body.is_valid()) {