The RStan license is irrelevant. Just because PyStan was derived from RStan, doesn't mean we have to release them both under the same license. If we own a piece of IP, we can license it to different people under different licenses.
For example, MySQL released their software under the GPL and also sold non-GPL licenses. No issue whatsoever and no conflict because they owned the IP. A third party who used it under the GPL couldn't remove the GPL, but the owners of the IP can license it however they want.
If a third party had written RStan, we'd have to abide by their license or negotiate a separate license.