Leonardo may have been a nonconformist, but he was still in need of a patron. And his patron at the time he painted his Last Supper, Ludovico Sforza, was in need of some clout to give him and his family name some respectability. So he tasked Leonardo with creating something brilliant that would do just that, which resulted in the Last Supper we know today as THE Lsst Supper. It wasn't the first Last Supper, but it's the best known and most revered because Leonardo put everything he knew about perspective and light into this one piece.
I know people want to believe there's more to history than what we're told, hence why authors like Brown can sell nicely packaged garbage like DVC, but it's no more complicated than that. Leonardo was an artist needing to sustain his livelihood and Sforza was the purse that kept paying out so long as the work was agreeable.