### 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)
TILEMAP_CALL_FOR_LAYER_V(p_layer, TypedArray<Vector2i>(), get_used_cells);
}
TypedArray<Vector2i> TileMap::get_used_cells_by_id(int p_layer, int p_source_id, const Vector2i p_atlas_coords, int p_alternative_tile) const {
	TILEMAP_CALL_FOR_LAYER_V(p_layer, TypedArray<Vector2i>(), get_used_cells_by_id, p_source_id, p_atlas_coords, p_alternative_tile);
}
Rect2i TileMap::get_used_rect() const {
	
	bool first = true;
	Rect2i rect = Rect2i();
	for (const Ref<TileMapLayer> &layer : layers) {
		Rect2i layer_rect = layer->get_used_rect();
		if (layer_rect == Rect2i()) {
			continue;
		}
		if (first) {
			rect = layer_rect;
			first = false;
		} else {
			rect = rect.merge(layer_rect);
		}
	}
	return rect;
}
void TileMap::set_light_mask(int p_light_mask) {