Oh, the sets were definitely used, just upgraded for the big screen. That's why they were able to keep using the same sets for nearly 30 years, redressing them for multiple movies, then TNG, and then Voyager. Movie sets are flimsy, meant to be used for a few weeks and then disassembled, but TV sets are made to last for years of regular use. So the fact that the Enterprise sets were built for Phase II was what enabled them to stay in use for decades. Plus, of course, the pilot script was reworked into TMP, but it was rewritten so heavily that maybe that made little difference from a time and budget standpoint. Not quite. The version in the novelization draws on the Memory Wall sequence in its descriptions of V'ger's interior, but the action conforms to the final filmed version, with Spock going in alone and being sent back just after Kirk exits the airlock.