My preference for "normal" dirt drops like the WTB and Nitto ones, is aligned with the flare of the bar - so rotated a bit from vertical. Part of the reason for the flare is that it more closely mirrors the natural angle of your grip. If you rotate the bar-end shifters vertically, you have to rotate your hand back to the un-natural vertical every time you shift. (Well, depending on the position of the lever and which way you're shifting, you may not "have to" rotate your hand, but then it feels awakard.)
However, on REALLY wide and flared dirt drops like the Salsa Woodchipper, I've decided I don't like bar end shifters at all because they stick out to the side too much when installed in this proper alignment. Every time I lean the bike against something, and half of the times when I mount or dismount the bike, I end up bumping the shifter into another gear.
Woodchipper has a long enough grip at the drop part of the bar to not to "require" the bar end shifters. I'm not sure how something like a Midge would work, where the grip is too short without the shifter, but people seem to adapt.