I suggest you take a little time to remove the soil on top and dig down until you find the primary roots. You might find out that you have a couple of inches of trunk below the soil level. As for the graft it may get larger with time and create an unsightly mounded mass as I have seen on many European hinokis. Jonas Dupuich has several blog entries on his website where he did this and found both trees he had bought were grafted so he attempted to air layer them above the swelling. Not sure what final success he had doing that.