In the Stone Lantern Pine Masters book the black pine article says that there is an "optional" pruning of the roots you can do after the initial cutting, of course they don't really say when to prune, or give any more details (unfortunately).
In Bonsai Today #12, however, different authors focused a little more on their approach for doing seedling-cuttings and developing large-trunk black pines. Instead of doing a second "cutting" like in the Masters Pine book, they waited 4 weeks after doing the initial cutting to repot and arrange the roots. This way, the pines could use the rest of the growing season and early winter to recover, and have a very strong growing season the next year.
Using the Master's Pine method, by contrast, the pines would be repotted/wired/roots arranged in spring of the 2nd year, likely leading to more recovery time and a later first flush of growth during the 2nd year.
Another reason why you'd probably want to rearrange roots early is that you'd rather kill the plant earlier than later (if at all). It's depressing to spend all winter nurturing/planning for your pine only to kill it in spring by doing the dramatic Masters Pine approach and repot + wire. Of course, you could just follow the Masters Pine book, but space things out a bit more, doing the repot in spring and waiting another year to wire. All good things to experiment with.
I would do all three options, leave some seedlings alone, try some the Master's Book way, and also experiment doing the Bonsai Today #12 way. That way you'd really learn something for future seedlings.
