### 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::OBJECT, vformat("navigation_layer_%d/%s", i, PNAME("polygon")), PROPERTY_HINT_RESOURCE_TYPE, "NavigationPolygon", PROPERTY_USAGE_DEFAULT);
			if (!navigation[i].is_valid()) {
				property_info.usage ^= PROPERTY_USAGE_STORAGE;
			}
			p_list->push_back(property_info);
		}
		
		p_list->push_back(PropertyInfo(Variant::NIL, GNAME("Custom Data", "custom_data_"), PROPERTY_HINT_NONE, "custom_data_", PROPERTY_USAGE_GROUP));
		for (int i = 0; i < custom_data.size(); i++) {
			Variant default_val;
			Callable::CallError error;
			Variant::construct(custom_data[i].get_type(), default_val, nullptr, 0, error);
			property_info = PropertyInfo(tile_set->get_custom_data_layer_type(i), vformat("custom_data_%d", i), PROPERTY_HINT_NONE, String(), PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_NIL_IS_VARIANT);
			if (custom_data[i] == default_val) {
				property_info.usage ^= PROPERTY_USAGE_STORAGE;
			}
			p_list->push_back(property_info);
		}
	}
}
void TileData::_bind_methods() {
	
	ClassDB::bind_method(D_METHOD("set_flip_h", "flip_h"), &TileData::set_flip_h);
	ClassDB::bind_method(D_METHOD("get_flip_h"), &TileData::get_flip_h);
	ClassDB::bind_method(D_METHOD("set_flip_v", "flip_v"), &TileData::set_flip_v);
	ClassDB::bind_method(D_METHOD("get_flip_v"), &TileData::get_flip_v);
	ClassDB::bind_method(D_METHOD("set_transpose", "transpose"), &TileData::set_transpose);
	ClassDB::bind_method(D_METHOD("get_transpose"), &TileData::get_transpose);
	ClassDB::bind_method(D_METHOD("set_material", "material"), &TileData::set_material);
	ClassDB::bind_method(D_METHOD("get_material"), &TileData::get_material);