The girdling root issue with deep planting has to do, as I understand it, with the roots being able to grow up over the top of the major spreading roots if there is soil or mulch available for them to grow into. If the major roots, at least those in that region of rapid taper close to the trunk, are near the surface, those roots that try to grow over the top and eventually girdle the main roots or stem are air pruned. If you have a volcano of mulch around them this supplies the well aerated, moist environment that the roots will love to grow in.
Another issue is planter beds around the base of a tree. This will keep the collar unnaturally wet and lead to the same problems.
In the a cooler climates, such as ND, the mulch volcano creates a great cafeteria for mice and such during the winter. They can eat in with out having to go out in the cold. Even the mice up here are smart!!!
Here are some videos about root crown excavation. The number 10 one deals with the above issues. I have not looked at all of them, but what I saw I think is a good basis for discussion.
http://wn.com/Root_excavation
As to the issue of whether or not to bury a graft, I tend to say to follow the rule of having the root collar at the surface. Again as was said before, the bark above the collar is designed to be in a dry environment, that below the root collar is adapted to a moist environment. Fungi, bacteria, nematodes, and other critters are going to be better able to access the xylem and phloem that is near the surface, if the environment around it is conducive to their thriving