I agree with you, but again though, you could have a game from Flacco--or Cutler, Stafford, anyone who throws jump balls downfield--where they hit two 40, 50 yard bombs but miss on six more of them. When you have Brady and this offensive scheme there's almost no reason (behind needing quick scores, end of the half or needing a comeback) where you ever need to look downfield. The dink-and-dunk offense gets them to the same place without the threat of INT's and missing downfield on 2nd-and-10 and missing out on a first down.
So let's say QB1 goes 3-of-10 (for 110 yards total) on deep balls, his team gets big yards on three passes but miss out on first downs a few times on some of the other throws. Meanwhile QB2 goes 1-of-4 (for 50 yards) on deep balls, similar completion percentage and yards/att, but far fewer shots downfield, which can stall a drive or lead to a pick. The rest of the game they have similar stats, except QB2 has more short completions for 4-6 yards and a first down.
I'm taking the QB2 any day of the week and twice on NFL Sunday, regardless of an inferior yards/attempt (which, again, is a factor in passer rating). Fewer risky deep passes, constantly moving the chain, wear the defense out. And that's what Brady does, the occasional seam pass to Gronk or deep shot to Edelman but otherwise it's death by a million paper cuts.