### 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)
r_changed = false;
#ifdef DEBUG_ENABLED
	if (rect_cache_dirty) {
		Rect2 r_total;
		bool first = true;
		for (const KeyValue<Vector2i, CellData> &E : tile_map) {
			Rect2 r;
			r.position = tile_map_node->map_to_local(E.key);
			r.size = Size2();
			if (first) {
				r_total = r;
				first = false;
			} else {
				r_total = r_total.merge(r);
			}
		}
		r_changed = rect_cache != r_total;
		rect_cache = r_total;
		rect_cache_dirty = false;
	}
#endif
	return rect_cache;
}
HashMap<Vector2i, TileSet::TerrainsPattern> TileMapLayer::terrain_fill_constraints(const Vector<Vector2i> &p_to_replace, int p_terrain_set, const RBSet<TerrainConstraint> &p_constraints) {