At Kouka-en, we rarely repotted or acquired bonsai with field soil still attached. Even field grown trees and shrubs grown for bonsai were washed of field soil and repotted before we got them. I'm confident we would not leave it in the center mass of the tree as the "heart" (core of root mass under the trunk) is important for the health of a plant.
We did on occasion get trees in large terra cotta or grow boxes with crappy media throughout the container; generally from hobbyists' collections. We would bare root as much as possible for a given species, perforate the root mass, and plan on another more aggressive repotting in 2-3 years.
Such is the way of things at a more specialized bonsai garden. With the black pines in the worst of media conditions, we bare-rooted sections with patches of dead roots and whittled away at the old media. It really depended on the ratio of foliage to root mass when removing the old media. As much as possible. Junipers' root systems were always kept more intact, but perforated more. The rambling nature of juniper roots on collected shimpaku lead us to cut less larger roots and clean out around them more.
We do not mess with the surface roots on Ezo Spruce; they tend to stall for a year or so if the surface roots are raked. Given that we never did it, I can't say that it does. Given my teacher repotted a ton at Mansei-en I am inclined to believe him
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