As I understand it, the NFL got the players to agree not to pursue any collusion claims against the owners related to those punishments. Why would the owners ask for such an agreement if they thought it was legal to ban teams from backloading contracts into the uncapped year?The argument of the league, as I have understood it, was that the contracts signed during the uncapped year were structured to impact other years, where there was a cap in place. That is a pretty legitimate argument on the facts of the situation---these were not one-year deals. At all relevant times the league management council was the body who determined cap interpretation, and at all points defined it in a way that made those contracts violative of the cap, including warning teams not to do exactly what the Cowboys and Redskins did.
What you say about why the owners did this makes sense, but you're giving the argument of only one side in an adversarial situation. I still think the punishment of DAL and WAS speaks more to the majority of owners' ability to punish teams that act to reduce ownership profit, than it speaks to teams' likelihood of getting randomly screwed over by a rogue commissioner or small group of owners.