Very good question and worthy post. Personally being an old school seat of the pants kind of guy I tend to go with what I know. And I know two things.
1. Toyota says down.
2. I've always put it UP, because that is how I was taught by Walter P. Chrysler in 1917. His goons the Dodge Bros agreed, but they may have been sucking up.

I am planning a timing belt job at the end of summer and I'll have to decide. Personally I don't believe the whole 15 degrees of swing fantasy. Come to think of it I don't believe any fantasies, although I do enjoy some of my own. I especially like the one where my 3.4 gets better gas mileage than my 3RZ. But I digress.

It makes so much more sense to me to have the valve at 12:00 because the air bubbles tend tow move upwards. But that isn't a scientific explanation, just sort of eye balled. I'd be willing to consider a valid explanation to follow the manual. Hey, maybe it was a misprint? Or the guy was pissed off at his boss and figured he'd live on in infamy by throwing us 3rd gen guys a curve. I'm sure he knew we'd be doing timing belts forever.

Hopefully someone truly "knows" the verifiable answer.