Installs on the AppVM should persist. If they do not, that is either a bug in rustup or a bug in Qubes OS. The install in the template not being usable in template-based qubes is expected, since rustup installs Rust to the home directory, not the root filesystem. It is also a bad idea, since it assumes you trust the TLS connection to the server and requires enabling networking. I recommend using Debian- or Fedora- provided Rust packages instead.