It is a safe bet that some of Tom's physical abilities have declined a bit, age 40 compared to, say, age 25. We might see that in a hypothetical physical skills challenge.
News flash: quarterbacking is not a physical skills challenge. Every physical skill related to quarterbacking has mental and preparation components to it as well.
Say that you move laterally a little slower than you used to, but you now recognize the need to move laterally far sooner than you used to, due to experience and better recognition. Net result: you get out of harm's way as well as before, maybe even better.
Say that your arm strength is a little less than it used to be. Now, though, you have continually perfected your throwing mechanics such that it takes less power to make the same exact throws than it used to. The better mechanics boost the accuracy as well. Net result: you throw the deep ball as well as before, maybe even better.
Say that your recovery from a game where you took a lot of hits is less than before. Now, though, you better see the hits coming, you take smaller shots by protecting your body better, so in total there is not as much to recover from. Perhaps you have also continually perfected your nutritional and training techniques to recover as well as possible. You don't slam beers like Brett Favre did. You don't eat junk like most everyone else does. Net result: you recover as well as before, maybe even better.
Late 20s may be your physical peak, but if the mental acuity keeps rising and rising, it makes up the difference.
This won't go on forever, but it is silly to take wild guesses in the direction of cheating. He's an outlier in terms of aging, but he's a much an outlier in hard work, preparation, nutrition, dedication, and determination. These factors combine to explain his continue excellence just as well. But it is not a hawt take.