You are looking at the the issue from a different perspective.
What's being said is that you put your best hitter (and by best, it's the guy with the highest OBP) in the #1 spot, because there's an extremely strong correlation between getting a guy on base leading off an inning and scoring runs. What Kimmi in particular is debating is the value of having that hitter batting 3rd, when it's a lot harder to score a run if said hitter gets on with 2 outs and no one on.
Although I don't completely adhere to her ideas, I see what she's saying. In my opinion, you should put two high-OBP contact guys one and two (Betts and Xander) followed by your best all-around hitter (OBP + SLG + speed, or Pedroia) followed by your biggest masher (Ortiz) and guys with the ability to produce runs (Hanley) then figure out the rest of the lineup by splits/overall hitting ability. Then again, that's just how I see it.