The point the article brings up is the league had a lot to gain by winning the case and by doing so they wouldn't have to go on this "apology" tour they're doing now. There's a convincing argument that they wouldn't settle if they thought they would win. They didn't settle during Deflategate and that was the league's poster boy.
Deflategate wasn't about collusion. The stakes aren't comparable at all. They didn't give a damn about Brady trying them over some nonsense. Neither side was going to be damaged regardless of the outcome. Losing the collusion case meant a 9 figure payout and a violation of the CBA.
It's in the interest of both parties to reach a settlement because the risk is too great on either side.