In response to moonslav59's comment:
How many times do teams miss the playoffs by 1-3 games?
Even if that is all a line-up matters, it is still important to do the best you can.
Just batting 3rd instead of 4th gives a batter 15-20 more PAs in a season. That alone can be the difference maker in a game or two. OBP up first, speed in front of slow, power behind OBP, etc... It all adds up.
Absolutely, that 1 or 2 games can mean the difference between making the playoffs or not.
However, 1 or 2 games is the difference between the optimal line up and the traditional line up. The difference between one traditional line up and another traditional lineup, where someone like Victorino is moved from the #2 spot to the #7 spot, is typically about 3 runs a season.
It is likely more beneficial to put a batter in a spot where he is comfortable than it is to put him in spot because he fits the prototypical profile for that spot. It is also likely more beneficial to split up your LHH than it is to put hitters in their prototypical spots.
Unless a manager is willing to go against the grain and do something as seemingly whacky as batting Papi first or batting a pitcher 4th, it really doesn't matter what the line up is.
Many of the things that managers go by in setting line ups are accepted for no other reason than that they have been done forever. That doesn't necessarily mean they are right.