^^^ definitely, you could go the $600 tune and find they are only expecting to tune it and be done, if problems arise well thats outside of the quote.
the $1200 tune is probably taking into consideration needing to check over the newly installed parts, double check things and then do a tune, nothing unexpected should arise in this instance, unless its something major, but then that 'something major' would happen in either case..
report back how it goes...