This was their logic:
When the 63rd st tunnel was built, you are correct in that it was meant to serve as a conduit for NYCTA trains to and from Queens. That said, it wasn't supposed to be solely 6th ave trains through the tube. The line was built as part of the Program for Action, a major subway expansion package proposed but never fully executed in the '60s and '70s. Aside from 63rd st, the MTA proposed building a bypass line in Queens, and, crucially for this discussion, a second avenue subway. From that time, SAS had been planned with connections to the Broadway express tracks -- hence the extension of them to 63rd -- but also to Queens. With the additional capacity provided by the Bypass, there were supposed to be three SAS services: the equivalent of the modern day Q, running from northern SAS to Broadway, a sort of T train, running all the way down the avenue, and then a third service, connecting points in Queens with SAS via the bypass and 63rd st. To facilitate this connection between SAS and 63rd, the 63rd tunnels were stacked where they cross Second Avenue, and provisions for turnouts built, which would allow SAS trains to join seamlessly without having to construct a more complex flying junction. This had the additional benefit of facilitating F/Q cross platform transfers, and the subsequent separation of the F and Q lines heading west.