Having his daughters also wield power is just another way for him to continue expanding power without having to give anything up. Instead of giving his daughters up to other nations, his daughters would represent part of his expansion as they wielded their own governance. It's a preferred strategy. I'm sure he didn't hold much esteem for his descendants that weren't very efficient in their jobs though. He cares more about efficiency over traditions. He puts effort into making a useful enemy become his ally instead of trying to denigrate them.
Genghis Khan raised the status of women in positions of prominence and especially his daughters. I believe this to be the first time female human was elevated to such stature. Of course, it would be naive of anyone to think that his reasoning was to, in effect, be a forerunner with regards to raising the general esteem of females he remains a figure in history who probably put the foundation down for a chance of a female U.S. President.
People often forget that outlaws and individuals deemed as morally and ethically reprehensible, live outside of societal constraints. Lack of reverence works both ways. With the knowledge of Khan's discount for society's moral standards, it would not be difficult to believe in his discount of preconceived notions that women would be unfit for leadership. It would seem that all he wanted was perhaps loyalty, and the individuals who could perform the job in the way he thought was best.
By giving his daughters positions of power in his empire Genghis Khan was indeed progressive for his time. While his sons held more powerful positions, Genghis Khan's daughters were given their own powerful roles, something rare for women of the era to be allowed. Their marriages strengthened alliances, but they also played the role of ruler and even helped in defending the empire.
There's that old statistic that 0.5% of the worlds population is related to Genghis Khan. If this is the case, I think we can assume that he was a man who definitely didn't discriminate when it comes to the opposite sex. However, I'm not sure if history paints him as a figure for women's rights.