Yes, the NFL Players Association agreed since the very first Collective Bargaining Agreement that the Commissioner will have final say over punishment imposed on players for infractions against the integrity of the game. But the Commissioner still must be independent and unbiased in exercising his authority over the process.
If the Commissioner is being pressured by one or more owners to resolve the case a certain way, his ability to be independent and unbiased becomes undermined. As PFT recently reported, multiple influential owners have been trying to influence Roger Goodell’s decision in the Tom Brady appeal.