I must admit to being a bit anal about shifter position on the bar. Its because I am anal about my fit on the bike in general and to me shifter position is critical to comfort on the bike. OP...there is no rule per se. I always look at how top riders ride and have included their position below. I would say most pros ride with the shifter turned up on the bar and different than factory suggested orientation. This is true of me as well. If the top of the bar is level with the crotch of the hood, it doesn't feel as good and places more pressure on my outboard heel pad and ulnar nerve. So I like the hoods a bit proud of the handlebar to localize more pressure between my thumb and forefinger. Take note there is a major difference how bars are shaped in profile which affects the interface to the hoods. Also there is a pretty good disparity in how pros ride as well...including the bar shape they prefer. The most pronounced old school position is Armstrong's set up...I show an early handlebar when he rode Dura Ace. His later Sram position is more like the others.

The whole discussion about shifter position actually relates to how bikes have morphed in sizing and how shifters used to be positioned more down the front curve of a deeper hooked handlebar. Compact bars have in effect lowered the handlebar position with the shifters being now mounted higher on the bar....for essentially the same net position....tops being perhaps the most changed (lower)...old school deep hooks and shifters are pretty close to modern compact position.