### 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);
	Dictionary dict = p_value;
	tile_data->set_constant_linear_velocity(physics_layer, dict["linear_velocity"]);
	tile_data->set_constant_angular_velocity(physics_layer, dict["angular_velocity"]);
	Array array = dict["polygons"];
	tile_data->set_collision_polygons_count(physics_layer, array.size());
	for (int i = 0; i < array.size(); i++) {
		Dictionary polygon_dict = array[i];
		tile_data->set_collision_polygon_points(physics_layer, i, polygon_dict["points"]);
		tile_data->set_collision_polygon_one_way(physics_layer, i, polygon_dict["one_way"]);
		tile_data->set_collision_polygon_one_way_margin(physics_layer, i, polygon_dict["one_way_margin"]);
	}
	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());
}
Variant TileDataCollisionEditor::_get_value(TileSetAtlasSource *p_tile_set_atlas_source, Vector2 p_coords, int p_alternative_tile) {