Even if (that's' a big if in my mind) Brady liked them below 12.5 PSI, then I don't think they did anything to alter the footballs. To me, it sounds like the rubbing process created additional heat that would allow the refs to measure at 12.5 PSI and then (over time) the balls would naturally cool to make them slightly below 12.5 PSI for game time.
Now, we've herd from several groups for and against temperature changes affecting PSI, but I don't think one person (or even the Wells report?) discusses how the Patriots prepare their football. This is the possible angle and the grey rule that Brady could run with.
did they deliver valid footballs to the Refs, I would think so.
were the balls capable of being reduced without the need for anyone to alter them. I think that is entirely possible.
Similarly, if Rodgers likes his with more pressure, I think he'd be able to put cooler air in and it would naturally inflate after the temperature normalized.