There's two points I would add:
First, the 63rd Street tunnel was planned and built as a double-level tunnel to be used by NY City Transit subway trains on the upper level and Long Island Rail Road trains on the lower level. The lower level tunnels were designed to accommodate LIRR M-series MU cars. This is from the October 11, 1973 edition of the
New York Times:
Crouching close together deep under Welfare Island [today called Roosevelt Island] yesterday, Governor Rockefeller, Mayor Lindsay and Dr. William J. Ronan, chairman of the Metropolitan Transportation Authority, touched off an explosive charge that marked the official "holing through" of the 63rd Street tunnel. The $69.5-million tunnel eventually will carry both Long Island Rail Road and New York City subway trains between Queens and Manhattan. Link to Times article
The second point is, at the time the tunnel was being planned the location of the new Long Island Rail Road East Side terminal was not yet Grand Central Terminal; it was to have been built at E. 48th Street and Third Avenue.