First off, I agree with you 100% that it doesn't make a whole lot of difference who bats where. That's a point I've been trying to make, ad nauseum I'm sure, since forever.
That said, while it's true that in those 20 or so extra bats that the lead of hitter gets over the #2 guy, he likely makes the last out far more than he hits a walk off, he is also the guy who is most likely to extend the game to the next batter if he has the highest OBP.
I'm not trying to argue whether Mookie should bat 1st or 2nd. It doesn't make much of a difference and I trust Cora's judgment. My main argument here is that in determining the lead off hitter, OBP is king, and speed does not matter much for a lead off hitter.