The biggest reason is that having a scope too high, or too low for your individual rifle makes it difficult to get your eye lined up with the scope with the gun mounted correctly.
But there are other reasons that determine the bullets flight. The bore will always be lower than your sights and will always be pointed slightly up in relation to your line of sight. When you bullet leaves the muzzle it will be traveing up at a slight angle and will cross your line of sight at some point around 25-50 yards from the muzzle. It will reach its apex at some point and begin to fall back down. When it crosses the line of sight coming down, that is the range your rifle is zeroed.
If your scope is mounted 2" above the bore vs the typical 1.5" that means the angle the bullet takes to cross your line of sight the 1st time is sharper. For extreme long range shooting this can be an advantage. At typical hunting ranges it could be a disadvantage. An AR rifle with typical iron sights has the sights very high above the bore. If zeroed at 25 yards it will again be zeroed at 300 yards. Good for long range shooting, but it will be 6"+ high at 100 yards and about a foot high at 200 yards. It does not reach its apex until after 200 yards because the sights are so far above the bore. With a typical hunting rifle with the scope mounted lower you can zero at 100 yards and never have the bullet more than 1" above or below your line of sight from 50 yards to 150 yrds and only be 2-3" low at 200, about 8-9" low at 300.
The ballistics programs need this information to accurately calculate trajectory.