Thank you TropicDude, for the link to the research article from Brazil.
Yes, it is the "secondary, weaker plants", the identical-looking clones, that are the most desirable plants to use for rootstocks, so as to achieve uniformity of growth in groves, thus achieving uniformity of care / economy of scale.
Nurserymen do have to patiently wait a few more weeks for the seedlings to achieve sufficient size to be grafted. And "stone grafting" is not usually a good option, due to inadequate seed reserves available to the clones.
Disentangling 40,000 seeds a year to look for cotyledons and different types of attachments is likely to require more labor expenditures than learning to recognize non-standard leaves.