For the sake of argument: for example IRL, all cell organelles are given to you by your mother. Some organelles, like mitochondria, have their own DNA that is entirely separate from all the DNA in your body - different than everything else that "make you you".
Could be that the Dunyain women are infected, accidentally or on purpose, with some special something. Could be a mutation in the mitochondria, or for some reason a special organelle, or a virus embedded in one of those organelles. These types of things could happen IRL. At any rate some change that occurs would only be passed from Dunyain mothers to Dunayin children. A Dunyain father and a world-born woman would simply never be able to pass along whatever it is that this change was. Never. (This is why there is a "mitochondrial eve", ie we can trace our genetic line back, from woman to woman, to a single mother of the species.)
Btw, the assumption would be that whatever makes the Whale-Mothers so big, and whatever it is that keeps the Dunyain male children relatively normal, is due to this special/mutated/extra organelle. When its lost, you get screwed up half-dunyain and relatively physically normal looking female children.
Also, the Rape of Omindalea, I believe, is exceedingly important. This is a direct causal link for nonman genetics in the Anasurimbor. We could further assume, then, that whatever this mutation or virus or whatever it is that makes Dunyain and/or Whale-Mothers is something that can only affect/infect/effect those humans that have their genetics intertwined with the Anasurimbor line. A species specific thing that always affected Nonmen, and their giant whale-like women that we conveniently never see, and found its way to Ishual.
That turned into a bigger post than I expected. Anyway, there are plenty of reasons why Whale-Mothers could exist IRL. Assuming that they can't, I think, is more of a knee-jerk reaction at the disturbia of the scene rather than any real thinking through of possibilities.
Anyway, this is only a worthwhile discussion if you believe that everything in Earwa is the same as it is in our universe. Its not. We've got magic, special metaphysics, and alien interbreeding genetics going on. There should be some way to incorporate any of that into the "why/how whale-mother" question. However, if you want earth/human genetics, there you go. If you want other options to make this happen, let me know. I'm sure several other examples can be found.