What is the seed starter composed of? Primarily peat I would wager. If so my next question is how long do you intend to leave them in the starter mix?So for my blackpines seeds, I got some $3.99 seed starter, and I should just put the seeds in the tray spots, keep them uncovered and watered, away from full sun (right?) and pray they all stay alive right?
If you intend to re-pot them quickly you might be all right with that product, and if you intend to follow the method that I outlined above all of the old roots will be removed anyway.
If, on the other hand, you want to leave them alone for the season you will need to start with pots that are large enough and provide a mix that has excellent drainage, which the starter mix probably does not. Perlite is a good component for seed mixes and is readily available.
If you follow the second method you will need to do a fair amount of work on the roots at the next re-potting. You will need to remove the taproot and arrange the roots you leave in a radial pattern.
By cutting the roots off this year and then treating them like cuttings you are really way ahead of the curve in producing a good nebari for the future bonsai. As I noted above this is not without some drawbacks as you will surely lose a good percentage of them. I lost some in the seed flat and about 40% of the remaining ones due to the root chop. But I feel that it was worth it to ensure good quality rootage. Then again I started with a lot more seeds that were collected for free so I was not so concerned about loss.