Here's one explanation. McNally and Jastremski knew Tom likes the footballs nearer the lower 12.5 psi limit. In the Jets game that year the balls were closer to 16 psi. It was Brady himself who showed the refs the psi parameters of 12.5 -13.5.
Since none of the gauges were calibrated to a known standard that night that's reason enough for the slight disparity in psi.
Regardless of how it happened it was an equipment violation subject to a fine of several thousand dollars per football. The Vikings were caught on camera warming footballs (increasing psi) on the sideline that December and were just warned with no fine or suspension.
And as we know Brett Favre was just fined for sending a dick pic to a woman and not handing over his phone (not cooperating).
The punishment is what's unprecedented. Like I said Brady has had an unblemished career. Why go after him worse than a woman beater? Especially with no direct evidence he did anything wrong.
Goodell was looking like an idiot with all the bad press over how he handled the domestic abuse issues. He decided to come down hard on Brady to show how tough he can be. And he had several owners wanting him to go after the Pats because they thought they got off too easy with Spygate.
So, in the end it became not a story of who dunnit (if anything was actually done in the first place), but a vendetta against the Patriots by jealous owners.
The Brady case did bring to light how ridiculous it is to have a commissioner with so much power he can disregard due process and act like a King.
Unfortunately the NFL is so popular that even an idiot like Goodell can't screwed it up even though he seems to try like hell with his malfeasance.