let's make it simple........my rifle will be zeroed in to hit where the cross hairs are aimed at at 50yrds.....now to shoot at something at 100yrds,i aim about 1 1/2 '' higher....that's what hornady told me anyway.. 
SS,
Your POI will be determined by how high your scope/sights are from the center of your bore. Hornady is only going by general information entered into a ballistics calculator. There is only ONE WAY to know the POI at a given yardage for a particular rifle/load and sighting system, that is to shoot it. You may be 2" low, but you may also be 2" high, or you could have the same POI at 50 yards and 100 yards.
Any sighting system sits above the bore,,,to get your rifle to zero, you must have your axis of your bore tilted upward,,,where the trajectory crosse the line of sight will be one zero,,,but you must remember "what goes up comes down" and you will have another zero down the line somewhere,,,so every rifle has two zero's,,,now with that in mind, the above item all factor into this,,,your bullet will cross your line of sight twice, on the way up and on the way down,,,you could still be on the way up at 100 yards and be hitting higher that at 50 yards,,,if your scope/sights are closer to the bore, this will not be as dramatic of a change, and your two zero's will be much closer together,,,if your scope is in a set of high rings 1-1/2"+ above the bore, your two zero's will be further apart, and the APEX of your trajectory will be much higher than your two zero's.
Hope that helps explain it, but there are several factors other than just the basic load information that determine POI. Hornady is only giving you the trajectory of the bullets path, your sighing system will be what determines the POI at given ranges along that path of trajectory. The only exception to this would be if you determined the APEX of the trajectory and made that your zero, everthing else would be below your line of sight before and after your zero.
