> why, given the same schedules, are women under-represented in the higher paying, higher prestige job?

Why do you believe they have the same schedules? There's no rule that says when a pilot follows one flight with another flight, all the flight attendants have to join him.

I don't think there's all that much inherent value in having several flights flown by the same pilot -- if anything, it's the reverse -- so I'd tend to suspect that the rarity of female pilots owes more to the fact that pilots come from the Air Force.