Essentially your LOS (line of sight) is higher than the LOF (line of fire, or rifle bore). If you zero in at 50 yards, you're making two straight lines (LOS & LOF) intersect at that distance.
Essentially, no. If by "LOF" = bore line, definitely not the way it works.
Here's a picture: The bore line crosses the LOS somewhere around 15yds or so for this example sighted in at 59yds.

Notice with the above example you're within 1/2" from 12yds to 65yds. Outside that, yes you have to compensate. And yes you might have to compensate a little less for lower mounted sights. But, you always have to compensate, to some extent, for the distance involved. Doesn't matter how high/low your sights are mounted. The trick is how "on target" do you want to be? You'll miss at long distances, just the same as you will at short distances if you don't take into account, bullet rise/fall.