First, he uses data from 2003, the height of the power and scoring explosion. SB's, obviously were less valuable then. With scoring down over a run a game and power down especially, SB's have more value.
Second, his charts of teams that stole lots of bases, and their overall run production, and of teams that were high scoring teams and their SB propensity, are pretty much meaningless. They tell us nothing. If he had turned that into one of my logic or stat classes, I would have failed him.
The first chart only tells us that teams that use SB's usually don't have powerful offenses. It doesn't tells us what their production would be if they didn't steal bases. Same with the second chart. If one wanted to know the effect that SB's have on a teams's production, the only accurate way is to chart their production in years that they do steal a bunch against years where the same team, with the same players, don't steal a bunch of bases. Of course that's impossible.
Third, having a speedy leadoff hitter is better than having him in the middle of the lineup, because he will be in scoring postion when your best hitters are at the plate. Then middle of the lineup hitters not only hit for more power, they just hit better overall.
Last season, the bottom the Reds lineup had 270 singles. The middle of the lineup, 346. That's 76 more hits. That's why you want your speedy leadoff hitter hitting in front of your best hitters.