It's not really that opaque, if you look at their site, they've written articles on how it works; and besides that, even if it was only one level deep, that's still better than no levels deep.
Without examining how things are weighted for importance, without examining the algorithms that determine weightings of this or that, you take these DVOA rankings on blind faith. Of course no advanced analytics purveyors disclose their algorithms for two reasons: they don't want them copied and they don't want them questioned.
That does help; although, historically, teams that give up more yards per play on defense than they gain on offense don't win 13 games. There is no single stat, or couple of stats that can really be pointed to as the definitive way to win (except injuries, those are a stat that will definitively point out losing).
If you want to go by yards then injuries flow into thos stats. But yards are looking at it backwards and you are correct in saying no single stat tells you what goes into winning and that would include a DVOA. Can you tell me what a 10 point difference in a DVOA equates to in the real world? Is it one point, points? Who knows.
The object is to look at that 13-3 team and assess how they got there. Otherwise, if you look at yards, for example as in this case you're left saying it didn't actually happen. But it did. You fall into highlightitis and fantasy falacies. There are widely varying ways of winning. The object is to look at how this team accomplished it.
So, what might DVOA be missing? Since Red Zone performance is rarely discussed, I have to conclude it is generally underappreciated. Is that the case with DVOA? We don't know, which is the point. Yards in the Red Zone, getting and giving, are simply more valuable. Kicking field goals all day, or worse failing on 4th. down in the Red Zone on offense or defense, isn't going to win a football game very often. Right up with Red Zone performance is giveaway/takeaway. The 2019 Packers rated highly in these categories. They were highly in yardage and possessions, efficient enough to win close games. The question is whether that is repeatable. Plus on the turnovers with Rodgers at QB is probably in the bank in any case. This begs another question: are turnovers, giving and getting, undervalued in DVOA or any other black box?
Of course we cannot dispense with big play scoring. Those are points on the board which translates to wins. But highlight-itis exagerates how often they actually happen.
Including playoffs the Packers scored 12 TDs of 20 yards or longer; the defense allowed 12. All of the season's point differential is attributable to Red Zone performance.
However 4 of the 12 big play TDs were by the 49ers, two passing in the first game, which is rather telling in terms of the defensive game plan for the playoffs. Then it was two rushing in the second, the first of them important on the first score of the game and setting the tone, with the Packers in a pass defense/blitz with one down lineman on 3nd. and 8. Of course the Packers were trying to get back in the game down 17-0 with the ball on SF's 25. Fumble, with all the air going out. Turnovers.... The SF story is more about being upside down on defending the big play, uncharacteristic of the rest of the season, failing to adjust to run-run-run, and then the turnover.
The Packers had a formula for winning that simply didn't work against SF, not just getting beat but beat down. While we can point to some personnel upgrades that might be in order after that game, the main problem is the final analysis is Pettine got out-coached, whether that's something imbedded in the scheme or just being upside down on game planning. Given what transpired in the free agency and the draft, one would assume the inside thinking is it's game planning which is correctable while scheme is not.
We can draw a parallel to the Kaepernick romp-a-thon, where Capers persisted in man D without a spy and Kaepernick ran all over him with DBs backs to play. Woodson was pretty outspoken about the failure to make adjustments. We don't have anybody quite so voluable on this team.