So this is why if you read the CNV studies and you look at the hits they identify, and how many subjects are covered by the identified hits, you find that like, maybe 2% of the cohort will have one of those specific identified hits and lose 2 IQ points or gain 2 kg of fat etc. So you can see how that would work out in embryo selection: you'd be able to avoid that loss, which is meaningful! ...in a tiny fraction of all embryos. On average, you'd just sequence them all, find no known pathogenic variant, and shrug, and use the SNP PGS like usual, having gained nothing.

Also, of course, WGS is substantially more expensive than SNP genotyping and more difficult to do on embryos.

That is relevant in pre-implantation diagnosis for parents and gene therapy at the population level. But for Qwisatz Haderach breeding purposes those costs are immaterial. There the main bottleneck is the iteration of selection, or making synthetic genomes. Going for the most typical genome with the least amount of originality is not a technical challenge in itself, right? We would not be interested in the effect of the ugliness, only in getting it out.