The scaffold branch height remains the same. The first scaffold branch height is usually about 3-4' above ground. As it ages is gets pulled down to the ground under the weight of the fruit. As the tree ages and higher scaffolds are grown the lowest scaffold is remove. Usually the scaffold just above the lowest is hanging over--and on top of--the lowest scaffold by this time. Also, people usually want to mow under the tree so lower scaffolds are removed to enable mowing. For deer apple trees, the deer will browse all limbs up to about 5-6 feet, probably killing all branches 5' and lower. You should prune the lower branches off to the first scaffold is about 5' high. Let the tree put its energy into growing upper branches rather than low branches that will get killed due to browsing. I always fenced my deer apple trees in until their lowest branches were at 5' high, removing the lower branches as the tree grew. Don't prune off the central leader. Let the tree grow fast upward.