According to the precedent of previous appeal hearing awards and federal court decisions, their system doesn't allow it. Goodell just completely sidestepped the issue of whether or not the system allows it by preventing anyone from actually reviewing the issue. He made a gamble that he and his underlings could 1) willfully disregard collectively bargained disciplinary policies (as well as basic fairness) in issuing the initial discipline, 2) short circuit the independent appeal process so that he could rule in his own favor that he did not violate the collectively bargained policies that he and NFL employees did in fact violate and that the lies used to support the discipline were actually truths, 3) forever seal off the evidence of this malfeasance from the public, and 4) either get Brady to accept a settlement or quickly win in court on the technicality of the limited scope of appeals to arbitration awards. Presumably he and his lawyers had not anticipated that Brady would steadfastly maintain his innocence and would not settle quickly, and the federal judge would not be keen to obfuscate the truth to the public in order to fight the NFL's PR battle for them. I still have no idea if Brady has a good shot in court, but I do know that the NFL has irreparably torn apart whatever shreds of their reputation they had left. No player will ever trust the league office going forward.
It never had to be this way. Consider that the NFLPA agreed to use the previous commissioner as a neutral arbitrator for reviewing disciplinary decisions, and that previous commissioner ruled in the player's favor. The NFLPA used to have at least some sort of trust and rapport with the commissioner. That is gone for as long as Goodell is in charge of the league office. Maybe for good. Who knows what repercussions that will have in the next CBA negotiations.