### 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)
RBSet<Vector2i> painted_set;
	for (int i = p_coords_array.size() - 1; i >= 0; i--) {
		const Vector2i &coords = p_coords_array[i];
		can_modify_list.push_back(coords);
		can_modify_set.insert(coords);
		painted_set.insert(coords);
	}
	for (Vector2i coords : p_coords_array) {
		
		for (int j = 0; j < TileSet::CELL_NEIGHBOR_MAX; j++) {
			TileSet::CellNeighbor bit = TileSet::CellNeighbor(j);
			if (tile_set->is_valid_terrain_peering_bit(p_terrain_set, bit)) {
				Vector2i neighbor = tile_map_node->get_neighbor_cell(coords, bit);
				if (!can_modify_set.has(neighbor)) {
					can_modify_list.push_back(neighbor);
					can_modify_set.insert(neighbor);
				}
			}
		}
	}
	RBSet<TerrainConstraint> constraints;
	
	for (Vector2i coords : p_coords_array) {
		
		TerrainConstraint c = TerrainConstraint(tile_map_node, coords, p_terrain);
		c.set_priority(10);
		constraints.insert(c);
	}
	for (int i = 0; i < p_coords_array.size() - 1; i++) {