There is a reason that there is a graft with rootstock below and scion wood above. Often it is about getting as many trees to sell as you can. Fruit trees openly hybridize and they do not come "true" from seed. If you want a Honeycrisp tree, planting a seed from a Honeycrisp apple will not likely end up as a Honeycrisp - probably possible, but highly improbable - maybe even better. The other main way to propagate pome fruits is to make cuttings. Many pome fruits do not readily root from cuttings and the ones that do are not all that reliable. Additionally, some selections do not seem to grow on their own roots too well in all environments. It has been deemed much easier to graft buds onto selected rootstock. Find an easily grown-from-seed variety that has the correct growing characteristics, and hopeful resistance to the diseases of the area, bud a desirable variety on the rootstock and viola - you have a tree you can produce cheaply and sell expensively. But perhaps most important nowadays, there is a growing reliance on advanced growing "systems" to produce the most fruit per acre and be easily and inexpensively harvested. That often involves reduced height trees. there have been a number of rootstocks found and/or developed that impart "dwarfing" characteristics to the variety grafted on top. What might naturally be a 30' tree at maturity, might be dwarfed by the rootstock to only 6' tall. Denser plantings, easier harvesting with less expensive means results. If the graft is situated at ground level, there is a possibility the top graft could sprout roots and those roots taking over. If you have a standard size top on a standard sized rootstock, that might not be a problem. But if you have 500 acres of high density planted, dwarfed apples, you don't want or need a lot of them converting to standard size. 3" is usually touted as a good distance above ground level. Higher could reduce vigor and could cause other undesirable results.
Now, if your trees is an "interstem", then the above is out the window. That means that a piece of stem/trunk has been grafted between the rootstock and the top variety. There will be two grafts on the tree trunk. These should be planted with the "interstem" partially buried in the ground.