### 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)
return collision_visibility_mode;
}
void TileMap::set_navigation_visibility_mode(TileMap::VisibilityMode p_show_navigation) {
	if (navigation_visibility_mode == p_show_navigation) {
		return;
	}
	navigation_visibility_mode = p_show_navigation;
	for (Ref<TileMapLayer> &layer : layers) {
		layer->notify_tile_map_change(TileMapLayer::DIRTY_FLAGS_TILE_MAP_NAVIGATION_VISIBILITY_MODE);
	}
	emit_signal(CoreStringNames::get_singleton()->changed);
}
TileMap::VisibilityMode TileMap::get_navigation_visibility_mode() {
	return navigation_visibility_mode;
}
void TileMap::set_y_sort_enabled(bool p_enable) {
	if (is_y_sort_enabled() == p_enable) {
		return;
	}
	Node2D::set_y_sort_enabled(p_enable);
	for (Ref<TileMapLayer> &layer : layers) {
		layer->notify_tile_map_change(TileMapLayer::DIRTY_FLAGS_TILE_MAP_Y_SORT_ENABLED);
	}
	emit_signal(CoreStringNames::get_singleton()->changed);
	update_configuration_warnings();
}
void TileMap::set_cell(int p_layer, const Vector2i &p_coords, int p_source_id, const Vector2i p_atlas_coords, int p_alternative_tile) {