IMHO, it's not a contradiction of logic, but a contradiction of objective.

Or even more subtly, means to objective.
Most of the time, the picture will look more "right" if the histogram peaks in the middle.
But by exposing to the right, then using post process raw "development", and adjusting the tone downward such that the peak is nearer the middle will yield a cleaner, less noisy image than the other, ultimately "equally exposed" image.
For me, it's a question of how important is the "cleaner" image? If not so much, meter your peak to where it looks right (middle-ish), and save your jpeg. If you want the absolute best your camera can deliver and are willing put in the "manual" effort required to get there, then EV comp your exposure to push it to the right and be ready to spend the time to perfect it when you get home.
I'll agree that I don't trust how it "looks" on the LCD unless A) I've got my highlight/lowlight "blinkies" enabled, or B) I'm really just using the LCD to see the histogram AND C) I know how I've got my default JPEG conversions setup, since that's the basis for your displayed histogram.
-Chris