I'm not sure, but I think the problem here is that you think we're arguing that defense does not affect the likelihood that any particular three point shot goes in. That's not what we're saying. Not all 3s are created equally. We know only too well that Zak Irvin is way more likely to hit an open catch and shoot 3 than a contested off the dribble 3.
What we are saying is that good three point defense over the course of a game and season will most accurately predict 3 pointers taken. Why? Offenses want open 3s and lay-ups/dunks, the most efficient offense. Take those away and the offense is left with other things -- some of which will be contested 3s, but many of which will be long 2s or contested 2s. That's why "a lot of long 2s" or "good 2 pt defense and a low amount of 3s" are generally recipes for good defensive outcomes.
But Maryland shot 18-39 on 2s (46%), and 15 3s; Iowa shot 22-50 on 2s (44%) and 19 3s in an overtime game. These aren't dominating defensive performances but play those games 100 times and more times that not MD and Iowa will score less than they did in the two games just played -- and would not be performances that would cause Michigan to drop 40 spots in kenpom's defensive rankings.
So with Walton defending Cowan -- sure his defense played a role in how likely it was for the shot to go in. Hell, if Anthony Davis is out there maybe the shot gets blocked altogether. But the fact that the shot went in doesn't mean that it was a good shot or even necessarily bad defense - it may have been. It doesn't mean that Michigan didn't get somewhat unlucky that it went down.
And I think proper communication and understanding of these principles could help Michigan's players ratchet up their intensity throughout the game. They have to understand that even if they play good defense late in the game, some of those shots are going to go in -- in fact, sometimes a lot of them will. They're not good enough and luck is haphazard enough that they need to play every possession (or at least the vast majority of them) with focus and intensity if they want a high probability of a good season.