Exactly. I once went to SportTrac (I believe that was it) to get the actual cash received figures for Manning and Brady. If you start with each guy's second contract, Brady's average annual cash received was only about $1 million less than Manning's average annual cash received (something like $13mil vs. $14mil). So the idea of Brady taking some sort of massive discount (at least relative to Manning) is very overblown.
You might want to check that again. Those numbers seemed off, or at least misleading, to me, when I thought on it. Manning was on his rookie deal for a lot longer than Brady was on his, for example. Tom got a renegotiated deal after just 2 seasons, while Peyton played out that entire 6 year rookie deal, and $55,389,794 seemed like a big number gap for just 2 "underpaid" Brady seasons (even if you ramped those two sub $300k seasons to $10m seasons, we'd be looking at a $35m difference, which would still be about a $1.9m difference per year over 18 year careers), so I played very sleepy junior mathematician. And, to look at as even a slate as possible, I looked at their 2004 and 2005 contracts, leveled out at 2005, and went from there.
If my math is correct (and it's late, so it may very well not be, and I apologize if it's not), from 2005 to the present, Brady has made $173,264,706. From 2005 to his retirement in 2016, Manning made $187,400,0000ish (I had to play a bit with the 2004 contract in order to make 2005 the even point, so I went with APY of his entire contract, rather than the specific outlay in 2004). So, from 2005-2015, Manning made an APY of $17,036363, while Brady has made an APY of $13,328,054. That's a difference of $3,708,309 APY. Again, that's if my math is right, and my apologies if it's not.
Tom Brady Contract Details, Salary Cap Charges, Bonus Money | Over The Cap
Peyton Manning Contract Details, Salary Cap Charges, Bonus Money | Over The Cap