I'm perfectly okay with the conventional wisdom within the statistical community believing that the Brewers are just lucky. Although, that article was written in George W Bush administration, so I'm not sure how conventional that wisdom is?
Also, I'm confused by your takaways from the article. For me, I pulled out this quote:
"Our [teams with the best productive] outmakers have a combined .531 winning percentage, with three 90-win teams and no 90-loss teams. The worst productive outmakers have a .457 winning percentage, one 90-win team, and five 90-loss teams."
So the article acknowledges that there IS a corrolation with winning based on productive outs, which isn't that much of a surprise. But unless I'm mistaken (and I very well could be), it seems like their methodology presumes that each situation where a productive out can be made, is equal. That the batter or baserunner involved doesn't impact the value of the outmaking event.
I acknowledge that I can quickly get over my head with statistical methodology, so I'm open to being educated on this.