You are right about the advice and recommendations with regards to not to bare root bonsai trees and that at every repot we should reduce it to a nice root ball, as has been suggested in one of the earlier answers before. This process will take forever to sort the roots out. A handful of us believe in bare rooting the trees and speed up the development of the roots.
There are a few of us who do bare root the trees at every repot to sort the roots out, remove any ugly and criss crossing roots and leave a radial pattern. This process speeds up the root development and also helps develop the surface roots. During this process all thick tap roots are removed as well. I bare root my bonsai trees at repotting and also nursery plants and remove all the soil by dunking the roots in water, followed by gently washing with a hose.
Bare rooting comes with risks that you may end up killing the tree. This risk can be reduced if you bare root when repotting in spring and also ensure that the roots are always wet, spraying them often to prevent them from drying out.
Another big myth in the bonsai community is to repot in spring only. I repot throughout the year. Again you have to ensure that the roots are wet throughout the repotting process. If any one wants to either repot and then also bare root at times other than spring, first do in Spring and then try it in the summer with cheap material and if you get that right then move on to other trees.
I have come under attack from well known bonsai experts for bare rooting trees, repotting in summer and autumn, and their followers have also been abusive on social media. Their argument is what is wrong with the traditional methods ? My own view is that change is well thought out tried and tested and it works, its progress. They do not like change and also the fact that they did not have the courage to do the things that a few of us are doing and pushing the boundaries.
This is Progress and I have received many positive comments on my YouTube videos from a Japanese nursery, that they are now learning from the west and they too are now re-potting throughout the year. Their channel link is:
There are many repotting videos where I bare root the bonsai trees and nursery stock. My channel link is:
Here is a link to one of my Malus Crab Apple tree which was in a training pot and at the repotting, it was bare rooted:
For more information and over 250 bonsai videos, visit my channel to pick up more tips and tricks at: https://goo.gl/R9IKFp