The only reason I can think of to leave the stump a little tall when trying to get the root ball is if it will help you get it out. Like a place to hook chains,cables or for the leverage. If you have the equip to dig it out may not be nessary. A fresh stump of much size comes out hard, I have a D6 cat and a JD410 hoe and still have a little trouble. I have found using a chain saw out 3 feet or so on the roots helps alot (chain is toast after). John