Your first article has a quote saying they use RPI SOS.
"4. Strength of schedule, especially non-conference strength of schedule. At least one team gets left out of the tournament almost every year primarily because of a very poor non-conference schedule. The NET does not have a strength of schedule output, so the committee is still using the RPI version."
Anyway, below is what the NCAA actually offers about how they calculate it, and you'll see the quality of the opponent is in the first factor, "Team Value Index," which they say is "An algorithm set up to reward teams who beat other good teams?" Based on the NCAA's own language, which would have more of a reward, for instance, playing the 250th best team or the 350th best team?
This isn't hard: SOS plays a role in the NET. Who you played, where you played them.
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As to this question:
I can't answer that explicitly because I don't know. He's certainly not saying to himself "Let's make a schedule to make it worse to get a good seed." Could have been scheduling issues with other teams, might be an AD reason. Could be they guessed wrong on programs. Could be he thought the five teams they were playing (UNC, Kansas, Gonzaga, Indiana, Texas) were just fine. You are giving him the benefit of the doubt, which is fair because he's won a title. He also got a 4 seed last year when the team should have gotten a 3 seed.
But mathematically, playing terrible teams makes the Team Value Index worse.