I think this both overcomplicates and oversimplifies it though. When Jeff Luhnow or Andrew Friedman or Theo Epstein get their top picks right is it because they listen to the scouts, hire better scouts, or are better judges of talent (or implementers of analytics) themselves?
And for all of Middleton's flaws/similarities, he's not actually meddling in the draft. The higher-ups who botched these drafts are Gillick, Amaro, Wolver, Almaraz, Klentak (I doubt Macphail even paid attention). It's not unreasonable for them to be involved, and they all personally scout too. I doubt they have actually overruled local scouts or cross-checkers with their picks though. Guys like Kingery or Moniak or Haseley probably had everyone's thumbs-up.
They just need better everything. But the fact that mid and low round picks sometimes out play high round picks is just a thing that happens all the time, to all teams. I seriously doubt the Phillies have actually been better at developing 3rd-20th rounders than other teams; they have probably failed at that just as much if not more as with the 1st and 2nds.