It always has been the userspace of the Jetsons which was closed source and tied to Nvidia's custom kernel. I have not heard from people running Jetpack on a different userland than the one provided by Nvidia. Companies/Labs that update the OS don't care about CUDA, Nvidia contributes to Mesa support of the Jetsons and some only need a bit more GPU power than a RasPi.
That said, you can probably boot a Debian or Gentoo system using the Nvidia provided kernel if need be.