I think it's a semantic issue of whether you should say the pin is above or below the nut. I think what's meant is that the nut has gone down so far that the cotter pin no longer engages with its notches. It sounds fishy that they should go down that much further unless you tightened them way way too much, or the knuckle was already worn, or unless there was supposed to be a washer. I'd be inclined to say you should pop them loose again if you can, and retorque them and see if things line up properly. If they don't, you may have to consider that the ball joint stud is stretched.
The torque spec for these is about what you'd expect to put on a wheel lug, which means good and snug, but not anywhere near to what you would put on, for example, the axle nut, and nothing that would require a cheater bar. There should be enough give or take in the torque spec so that if your nut doesn't line up with a hole, you can tighten it a little more until it does.
I'd suggest just putting a washer under the nut, but without knowing how much torque was applied to get into your current situation, I'd hesitate to recommend it owing to the possibility that the ball joint stud is weakened. It seems pretty unlikely, and if I were in this situation, I'd probably try retorquing and use a washer if needed, but I can't make that recommendation without some sense of how mightily that stud was overstressed or stretched.
edit to add: while I was writing this I see an impact wrench has entered the discussion. Definitely, pop them and try retorquing, but if they don't fit right on the second try, I'd play it safe and swallow the cost. An impact wrench, if it's working right, will go way way past the recommended torque, and I don't think there's any such thing as a convenient time or place for a ball joint stud to break off.
