### 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 enabled;
}
void TileMapLayer::set_modulate(Color p_modulate) {
	if (modulate == p_modulate) {
		return;
	}
	modulate = p_modulate;
	dirty.flags[DIRTY_FLAGS_LAYER_MODULATE] = true;
	tile_map_node->queue_internal_update();
	tile_map_node->emit_signal(CoreStringNames::get_singleton()->changed);
}
Color TileMapLayer::get_modulate() const {
	return modulate;
}
void TileMapLayer::set_y_sort_enabled(bool p_y_sort_enabled) {
	if (y_sort_enabled == p_y_sort_enabled) {
		return;
	}
	y_sort_enabled = p_y_sort_enabled;
	dirty.flags[DIRTY_FLAGS_LAYER_Y_SORT_ENABLED] = true;
	tile_map_node->queue_internal_update();
	tile_map_node->emit_signal(CoreStringNames::get_singleton()->changed);
	tile_map_node->update_configuration_warnings();
}
bool TileMapLayer::is_y_sort_enabled() const {