### 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)
property_info = PropertyInfo(Variant::FLOAT, vformat("animation_frame_%d/duration", i), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR);
			if (!store_durations) {
				property_info.usage ^= PROPERTY_USAGE_STORAGE;
			}
			tile_property_list.push_back(property_info);
		}
		for (const KeyValue<int, TileData *> &E_alternative : E_tile.value.alternatives) {
			
			tile_property_list.push_back(PropertyInfo(Variant::INT, vformat("%d", E_alternative.key), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR));
			
			List<PropertyInfo> alternative_property_list;
			E_alternative.value->get_property_list(&alternative_property_list);
			for (PropertyInfo &alternative_property_info : alternative_property_list) {
				Variant default_value = ClassDB::class_get_default_property_value("TileData", alternative_property_info.name);
				Variant value = E_alternative.value->get(alternative_property_info.name);
				if (default_value.get_type() != Variant::NIL && bool(Variant::evaluate(Variant::OP_EQUAL, value, default_value))) {
					alternative_property_info.usage ^= PROPERTY_USAGE_STORAGE;
				}
				alternative_property_info.name = vformat("%s/%s", vformat("%d", E_alternative.key), alternative_property_info.name);
				tile_property_list.push_back(alternative_property_info);
			}
		}
		
		for (PropertyInfo &tile_property_info : tile_property_list) {
			tile_property_info.name = vformat("%s/%s", vformat("%d:%d", E_tile.key.x, E_tile.key.y), tile_property_info.name);
			p_list->push_back(tile_property_info);
		}
	}
}
void TileSetAtlasSource::create_tile(const Vector2i p_atlas_coords, const Vector2i p_size) {