Well, one of Theo's tricks in Boston was to pay well over slot for guys that would fall due to signability issues, which, in theory is something the new draft rules will snuff out.
I'm not really sure if the Red Sox are doing the minor league thing that much more productively than other teams, they're just able to buy a better core of guys to build around. From your "why don't the Sox have anyone as good as Josh Reddick in the minors?" question, here's two players, try and figure out which is which...
Player A - Career .263/.307/.436 hitter, averages 23 HR, 73 RBI, 70 R, 21 D, 30 BB, and 127 K per 162 games played
Player B - Career .244/.300/.445 hitter, averages 23 HR, 66 RBI, 74 R, 29 D, 42 BB, 126 K per 162 games played.
Reddick is Player B. Dayan Viciedo is Player A. It seems like there's a bit of a case of "the grass is always greener on the other side," here.
What will make the Cubs rebuild work, whenever they decide to do it, is that they are still one of Major League baseball's money machines. They will eventually be able to pay for top-notch talent. They're not going to be able to compete as long as they pretend like they can rebuild the organization from bottom up. That basically never works in baseball.