WordPress has hooks to allow pointing the uploads location to a different directory, which you can combine with PHP stream wrappers to have a virtual filesystem

WordPress has hooks to allow pointing the uploads location to a different directory, which you can combine with PHP stream wrappers to have a virtual filesystem. (Source: I wrote the original WP/App Engine integration back when Google first launched support for PHP; I also maintain a plugin that does the same for S3, for our AWS hosting platform.)