Hasaki: You wrote, I've had pine or 'blaauw' juniper where the crown and interior area was all clay, not removing some or all, you will be trying to water a pot with two types of soil.
That's true, but the fact remains if you bare root a tree by the traditional methods of root hook and chopstick, just to get rid of a clay core, you are most likely going to lose the tree. However if you have placed the tree as I described in a screened planter of some sort though you are dealing with two different types of soil you do not have the over watering problems if you had only placed the tree in a box, bonsai pot or large pot. How do I know
I do it all the time with Maples, Shimpakus and Pines. I have been developing trees like this for over twenty years.
With my method you start working on the clay core, if there is one, the next time you work on the roots. So instead of a tree having to adjust from having all the soil removed, and all the micorihiza, and all the roots disturbed it only has to adjust from having a good portion of the original root mass removed. The screened plantes allow excelent drainege, airability and room for a new root system to develop from still active roots.
The problem with unequal soil masses existing in a single environment is, as you have mentioned, one of watering. However over watering is an almost impossibility with this type of planter. The porous bonsai soil drains rapidly and never holds on to excess water so it is possible to water the tree for the sake of the core if need be without worrying about the rest of the soil mix becoming water logged.