### 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)
for (KeyValue<Vector2i, TileAlternativesData> E_tile : tiles) {
		for (KeyValue<int, TileData *> E_alternative : E_tile.value.alternatives) {
			E_alternative.value->remove_custom_data_layer(p_index);
		}
	}
}
void TileSetAtlasSource::reset_state() {
	tile_set = nullptr;
	for (KeyValue<Vector2i, TileAlternativesData> &E_tile : tiles) {
		for (const KeyValue<int, TileData *> &E_tile_data : E_tile.value.alternatives) {
			memdelete(E_tile_data.value);
		}
	}
	_coords_mapping_cache.clear();
	tiles.clear();
	tiles_ids.clear();
	_queue_update_padded_texture();
}
void TileSetAtlasSource::set_texture(Ref<Texture2D> p_texture) {
	if (texture.is_valid()) {
		texture->disconnect_changed(callable_mp(this, &TileSetAtlasSource::_queue_update_padded_texture));
	}
	texture = p_texture;
	if (texture.is_valid()) {
		texture->connect_changed(callable_mp(this, &TileSetAtlasSource::_queue_update_padded_texture));
	}
	_queue_update_padded_texture();
	emit_changed();
}
Ref<Texture2D> TileSetAtlasSource::get_texture() const {