### 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)
TileData *tile_data = p_tile_set_atlas_source->get_tile_data(p_coords, p_alternative_tile);
	ERR_FAIL_NULL(tile_data);
	polygon_editor->clear_polygons();
	for (int i = 0; i < tile_data->get_collision_polygons_count(physics_layer); i++) {
		Vector<Vector2> polygon = tile_data->get_collision_polygon_points(physics_layer, i);
		if (polygon.size() >= 3) {
			polygon_editor->add_polygon(polygon);
		}
	}
	_polygons_changed();
	dummy_object->set("linear_velocity", tile_data->get_constant_linear_velocity(physics_layer));
	dummy_object->set("angular_velocity", tile_data->get_constant_angular_velocity(physics_layer));
	for (int i = 0; i < tile_data->get_collision_polygons_count(physics_layer); i++) {
		dummy_object->set(vformat("polygon_%d_one_way", i), tile_data->is_collision_polygon_one_way(physics_layer, i));
		dummy_object->set(vformat("polygon_%d_one_way_margin", i), tile_data->get_collision_polygon_one_way_margin(physics_layer, i));
	}
	for (const KeyValue<StringName, EditorProperty *> &E : property_editors) {
		E.value->update_property();
	}
	polygon_editor->set_background(p_tile_set_atlas_source->get_texture(), p_tile_set_atlas_source->get_tile_texture_region(p_coords), tile_data->get_texture_origin(), tile_data->get_flip_h(), tile_data->get_flip_v(), tile_data->get_transpose(), tile_data->get_modulate());
}
void TileDataCollisionEditor::_set_value(TileSetAtlasSource *p_tile_set_atlas_source, Vector2 p_coords, int p_alternative_tile, Variant p_value) {