I will be the first to acknowledge that some OC's are too committed to the run, even when it isn't working... but what the 538 model fails to account for is way too complex for a simple little analysis like presented:
Even if you're struggling in the run game, it's hard to fault OC's for not throwing into a dime package.
Does the model account for the fact that when you're up by say 14, you're going to run to kill the clock in the second quarter, the defence knows you're going to run, and you do it anyway and gladly trade the 2-3 yard run for an extra 45 seconds of clock burn. Or how about if you're playing from down 14+ and the defence is in prevent. Situational football has a big effect on the down and distance efficiency, and what is true in one quarter and for one score but not true for the preceding or proceeding quarter
I would tend to agree that NFL offences are very slowly modernizing in a way that should lend itself to more passing on first down, but that balance is so, so important. I agree with the original comment from ajh6w, their successes coexist because of the balance. But I think to try to boil it down to a simple analysis like 538 has down kind of ignores some of the game management aspects, which oversimplifies the idea. But first down passing is something I suspect we'll see continue to trend upwards, albeit slowly