Some of mine have had major over growth. Like the scion double diameter of the rootstock. This hasn't caused any issues but staking would be a good idea. Personally I won't cover the scion with soil.

Windfall:

I have a 9 year old Northstar cherry. I bought it bare-root and not sure what rootstock it was budded on. As the
seasons passed, my cherry got much larger in caliper above the bud union than below it. Very noticeable.

As the tree aged, the difference in caliper just above and
below the bud union has diminished as the cherry growth rate has slowed and the rootstock has almost caught up in caliper. It has not been any health issue to the tree.
I suspect your cherry tree will do the same with age.

This is quite common on many plants that are budded/grafted
onto a rootstock. I see it even with ornamental pears
at the nursery I work at. Sometimes on shade trees too.

Thanks folks, I was not worried that it would prove a health issue per se, more that it would prove a structural issue under wind stress. Although from a health perspective, I do have a hard time envisioning just how well the trees "pipes" run through such a change were it to become more severe?

I am a wooden boatbuilder by trade, and if I were to put a rapid diameter change into a spar or other bending stressed piece....well it would be almost sure to break right there as a "hard spot" is created under load, which concentrates the forces applied to a single region instead of distributing them out.

It would ease my mind if they did equalize over time.

Fruitnut, why would you shy away from burying scion? For concern of disease issues being created by holding damp against the crown? Or because you would not want to lose controlling factors the rootstock provides?
I ask because I have intentionally burried many apple trees deep below the graft, knowing they would self root. It is a practice sometimes employed in the far north for a number of reasons. But I have never heard of it being used with anything but apple.

rob:

Primarily because of the tree size issue. Also I'm not sure the scion would root like many apples that want to root even exposed, ie burr knots. It might cause disease issues but I've no evidence of that.

Staking on the other hand if properly done is a sure winner.