...stroke (maybe more) is wasted, contributing nothing to charging the valve, due to compressed air being thrown overboard.
Meanwhile, the reason pressure-sensor-equipped ACPs sometimes require a skipped or extra stroke (relative to the nominal 3) is because the air expended with shot can (due to various factors both internal and external to the gun) be slightly less (e.g., 2.9 stroke volumes) or more (e.g., 3.1) than the nominal 3.0 stroke recharge volume. Therefore, over a series of shots, the recharge pressure can gradually creep up or down by that fraction of one stroke volume until, eventually, the sensor will indicate full pressure either one stroke "early" (after only 2 strokes) or "late" (after 4).
Consequently, the recharge pressure isn't perfectly consistent, but can vary from exactly 8 stroke volumes to slightly less than 9 - about +/-6% - with a consequent variation in MV (reduced substantially due to valve self-regulation effects) of typically ~+/-10fps. Not perfect, but still pretty good.
But in no case is air or pumping effort dumped overboard - i.e., wasted.