I understand what you are saying -- the problem is that this is an employment issue and not a criminal issue. So, the moment he destroyed his phone and withheld the phone from the league and "failed to cooperate" he subjected himself, not to criminal exposure, but to an "adverse employment" decision. If a league official had done that -- he would have been fired. Not gone to jail -but fired. There is language in the NFL owners agreements that personnel "must" cooperate with the league. I believe there is a similar provision in the CBA. Once Brady failed to cooperate, for whatever reason and by any method, he subjected himself to punishment by the league -- in this case a 4 game suspension. I don't care if he did it or not, or his fingerprints are on it our not (I do, but not for this purpose), once he failed to cooperate, he gets what he gets.
As for the phone itself, and any private information, again, the league never asked him to give it his phone. They said, let us sit together, side by side, and read your emails and texts only between you and other Pat personnel. They did not want to see, read, copy, etc his photos, contacts, other personal emails or texts. Once he refused to do that -- he failed to cooperate. Again, not a criminal offense like not agreeing to a search of your car or house without a warrant. But a violation of his employer's rules and procedures. There is no entitlement to play in the league.
And, yes, I think it makes a difference. As an official (25 years), we all know that there are two things an two things only that we all check every game at the HS Varsity, College and Pro level. One if the chains to make sure they are 10 yards. Two, the balls to make sure they are within the prescribed PSI. I my humble opinion, you screw with either of those two things, I would throw the book at you. If I discovered that a home team chain gain had adjusted the chain by a few inches after I checked in pre-game, they would be fired from the game, ejected from the field and the local AD would be notified to take appropriate action and I would never allow him/her to work the chains at another game I officiated. This is not an "equipment violation" as I have heard some suggest -- this was not failing to play with a mouthpiece, or a thigh pad. This was the ball.