Good question. If you were to plant it close enough to the graft, once it settles some, the grafted portion could root. Those roots are not reliable and would negate the dwarfing, or size-limiting properties of the rootstock it’s grafted to.
I’d suggest planting the rootstock at the ‘color difference’ on the bark, which indicates where it was growing before harvested. If that leaves the graft union too high for your taste, I’d plant it a ‘little’ deeper, leaving the bottom of the wrapped graft around 3 or 4 inches above the surrounding soil (just as you described doing). It can also depend on how high the graft was made on the rootstock; though I try to keep those I graft closer to the roots… to keep buds bursting from the rootstock and competing with the grafted scion above. I was one of the grafters.
And ask us those questions - most
of us are pretty friendly
. There was also an excellent revised ‘green flyer’ with after-care instructions at the grafting payment table. Did you take one? …and let me know if this is TMI
…though it appears to be my mo ~