The braking response definitely goes down as you move the pads down the slot. Lower pads have proportionately less mechanical advantage. But the R559s have a longer lever arm to adjust for the longer brake reach. They won't be as powerful as the same brakes would be with the pads at the top of the slot but they should compare to R539s with the pads at the bottom of the slot. In any event, the slot placement is a relatively small effect. The mechanical advantage mostly comes from the distance from the pad to the pivot point, which is larger than the range of pad adjustment.

FWIW, I've had R559s with 650B A23 rims working very well. What levers are you using?