I don't think it matters whether you have some seeding trunk below the graft. I often pull the seedlings further through the hole so roots start dividing right from the graft. The graft should still work whether you have trunk or roots in the hole, provided the roots are in the soil and the upper parts above ground.
Trunk can become part of nebari just as roots exposed to air develop bark and become part of 'trunk'. Try to think of branches, trunk and roots as a continuum rather than discrete separate entities.