A thought that occurred to me.
In general, judges like to rule on as narrow a basis as possible. Perhaps the judges want to completely avoid the "Article 46 makes Roger an evil god who can do whatever he wants, regardless of anything" because saying he can be an evil god is offensive to their sense of justice but explicitly saying that federal law X overturns Article 46 is also something they're not comfortable with.
So perhaps they're trying to develop a "Goodell had a decent enough reason to do what he did" foundation to enable them to say something like "We do not have to address issues A, B, and C because an impartial abitrator could reasonably believe Brady was involved because of P, Q, R. Thus we do not need to determine whether Goodell has the power to do anything he wants because he acted reasonably in this case. Berman decision vacated."
Not good for Brady, obviously.