### 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 (!tile_set) {
		return;
	}
	occluders.resize(tile_set->get_occlusion_layers_count());
	physics.resize(tile_set->get_physics_layers_count());
	for (int bit_index = 0; bit_index < 16; bit_index++) {
		if (terrain_set < 0 || terrain_peering_bits[bit_index] >= tile_set->get_terrains_count(terrain_set)) {
			terrain_peering_bits[bit_index] = -1;
		}
	}
	navigation.resize(tile_set->get_navigation_layers_count());
	
	custom_data.resize(tile_set->get_custom_data_layers_count());
	for (int i = 0; i < custom_data.size(); i++) {
		if (custom_data[i].get_type() != tile_set->get_custom_data_layer_type(i)) {
			Variant new_val;
			Callable::CallError error;
			if (Variant::can_convert(custom_data[i].get_type(), tile_set->get_custom_data_layer_type(i))) {
				const Variant *args[] = { &custom_data[i] };
				Variant::construct(tile_set->get_custom_data_layer_type(i), new_val, args, 1, error);
			} else {
				Variant::construct(tile_set->get_custom_data_layer_type(i), new_val, nullptr, 0, error);
			}
			custom_data.write[i] = new_val;
		}
	}
	notify_property_list_changed();
	emit_signal(SNAME("changed"));
}
void TileData::add_occlusion_layer(int p_to_pos) {