This is it in a nutshell. And while the union might have claimed collusion, as they often do while seldom actually persuing the claim let alone prevailing, the league killed two birds with one stone (it's called doing business as business is done, via compromise and concession).
The cap a week ago projected to as low as $113.5M and no more that $116M via the formula the two sides agreed to under the CBA of 2011. That had the potential to cost NFLPA members lots of jobs. In exchange for ownership agreeing to increase that number to $120.6M or a hair over last season's cap, as well as agreeing to credit the amount by which two teams were found to have manipulated the league's accounting cap rules in an attempt to gain competitive advantage back to the teams who did not, the NFLPA on behalf of it's members agreed not to even make the contention.
The league took no issue with the contracts because as written they did not violate any rule. The rule was violated in how the teams chose to account for a portion of the money paid to those individuals after the fact, in 2010 and going forward. The league never contended the contracts themselves were illegal, nor are they questioning those teams rights to overpay for said players as it turned out they did... Just how those bonus money contained in those contracts will be treated against the cap for accounting purposes, as they clearly informed teams it eventually would be.
The number of fans here with Don Quixote complexes never ceases to amaze me.