There was some puzzlement expressed in our ethics class last year over why anyone would (non-instrumentally) want power over others. My suggestion was a simple one: we all recognize the value of autonomy, or having power over ourselves. Perhaps the power-hungry person conceives of domination as an extension of their autonomy, in some sense. Or, put another way: if power over yourself is (egoistically) desirable, why not power over others? Think of it as expanding your capacities, or sphere of influence, or some such.
So I think the difference comes in at the moral level. It's not that powerlust is some thoroughly irrational fetish; it's just that the harmful effect on others makes it morally inappropriate to pursue.
(HT: Neil. Though as a hedonist he probably finds the value of autonomy just as incomprehensible.)