What's wrong with zip? It's fine. Maybe more than fine if it managed to be this popular for so many applications. From my understanding it's very good on floppy disk too
Basically there is no way to say to you operating system "hey, can I get a no-nonsense, don't what to have to come up with some other conventions that will be broken, way to have some additional storage and file system paths that are just for this file so I don't have to worry about name collisions?" I already have a perfectly good unique name under which I could stash information, but the posix standard basically prevents me from using that name as a way to safely namespace things that I need per file.
However, to your original point I have partially implemented this [0] using zip files on the read side. I treat the internal paths inside the zip file as if they are rooted at the zip file itself. I haven't implemented rewriting though.
0. https://github.com/tgbugs/augpathlib/blob/master/augpathlib/...