Who said any athlete should squat? I don't care if Howard squats or doesn't, but I think the argument given by that trainer doesn't suffice to rule out any form of squatting.
Regarding the length of the femurs and squatting, longer as what? If the lower limbs are relatively long as opposed to the upper body, then there can arise problems with squatting. But you still have to assess the individual's body structure as a whole, not only the femurs. And how about front squats, sumo squats, belt squats or bulgarian split squats? I've seen 7 footers front squat rather effortlessly. IMO all of these are better than a leg press as a primary exercise for athletic purposes.