Around here, we're advised not to even mulch up around the trunk of
trees. I've picked up the impression that
root and subsoil parts of trees are specially adapted to that environment. Above soil level the plant tissues are more suceptible to disease and insect pressures. They need the barrier of space and good airflow for the health of the plant.
Sorry, I think your tree would be happier if you unburied the trunk to the original root depth.
On the other hand, I've seen many naturally quite twisty trees. I wasn't under the impression that it was anything but a cosmetic flaw. What leads you to believe that a twisty trunk is less able to support the developed weight of the tree? Not saying you're wrong, just interested in learning something new. Someday I might need this information myself.