It's always made a little sense to bat Bonds third. It means more plate appearances over the course of the season and a guaranteed first inning at-bat. Bruce Bochy likes the idea, and now Bonds seems to be on board after all these years:
These simulations don't take into account some of the little things, such as Benji Molina running like Don Zimmer chained to a Volvo. Also, note that other lineups simulating better than the one we'll see in April include variations that have Randy Winn batting cleanup, so maybe the whole lineup construction business is to be taken with a grain of salt.
Long story short: It just doesn't matter much.
Short story long: I'm starting to dig this Bochy cat.