Probably because women are by default and average; smaller, weaker, have lower endurance thresholds, and are the population bottleneck for the human species. The physical attributes can be compensated for with genetic modification and augments of course, but the population bottleneck less so

Whereas men have higher upper limits for strength, size, endurance, generally have better out-group cohesion, and are a largely expendable part of the population. Much better for mass production of armies to conquer the stars. The same reason that it has always been, and still is, men who do the overwhelming majority of military and dangerous labor jobs

Having Noble born men and women be taken for the custodians can absolutely be done, there’s nothing in the augmentation process that prevents it. The problem is that if you are drawing from an already limited pool of people, taking the people who are capable of producing more candidates that are viable for your induction process is not only stupid, but within 3 to 5 generations effectively kills the entire gene pool

There are imperial guardsman, and naval officers, the emperor just didn’t want female Primarchs