### 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)
if (p_layer >= 0) {
		TILEMAP_CALL_FOR_LAYER(p_layer, notify_tile_map_change, TileMapLayer::DIRTY_FLAGS_TILE_MAP_RUNTIME_UPDATE);
	} else {
		for (Ref<TileMapLayer> &layer : layers) {
			layer->notify_tile_map_change(TileMapLayer::DIRTY_FLAGS_TILE_MAP_RUNTIME_UPDATE);
		}
	}
}
#ifdef TOOLS_ENABLED
Rect2 TileMap::_edit_get_rect() const {
	
	if (layers.is_empty()) {
		return Rect2();
	}
	bool any_changed = false;
	bool changed = false;
	Rect2 rect = layers[0]->get_rect(changed);
	any_changed |= changed;
	for (uint32_t i = 1; i < layers.size(); i++) {
		rect = rect.merge(layers[i]->get_rect(changed));
		any_changed |= changed;
	}
	const_cast<TileMap *>(this)->item_rect_changed(any_changed);
	return rect;
}
#endif
PackedVector2Array TileMap::_get_transformed_vertices(const PackedVector2Array &p_vertices, int p_alternative_id) {