I don't think he's necessarily lying. His Cowboys will make him money no matter what. The salary space he used on Prescott was going to be used on someone. And he's not concerned with using that space to build a better team because he's delusional enough to believe he's doing it right.
Jerry sees other teams' starting QBs making similar to what Prescott is getting, knows that will continue to increase and believes he's justified in paying his "franchise" QB that way.
I think if we think he's lying, expect him to know he should have done things differently, we're giving him more credit that he deserves as a GM. I think he has no idea why it has been a bad move, partly because he wholly believes in his philosophy to pay your own and not spend much for free agents from other teams.