Well, you transplant them according to how much room the particular veggie needs, so more than just those holes will be used most likely.
Thanks for the info, greeneyes. So here is my understanding of the experiment (thanks for undertaking it fanfan):
OK, so the little guys are being sprouted (hopefully) in seed cups in situ in the place where they will eventually be transferred grow.
If they sprout, then after they have had time to get their roots started,then they will be transplanted out of their cup and into the slot where they sprouted, which the gardener presumably had selected to make sure the little guy has enough room for its toes.
Do I have it finally? :-D