Well regarding the whale mothers I think some of it is our world doesn't have gods or sorcerers but it does have human genetics. So people can pick up on that as being unrealistic. Your right Bakker does have an out with nonmen genetics, but it didn't sit well with me regardless of that. For one it seems to be getting rid of realism in favor of horror the Dunyain are efficient and amoral, and if the women are Dunyain as well there is no reason to restrain them and furthermore knowing what we know of human biology keeping women in such conditions is not conducive to a healthy pregnancy and bringing a child to term.
Lots of assumptions there. At what point has the surface of what has been revealed remained clear throughout the series? Good/bad/damned/saved... Things don't ever seem to be what they are in TSA.
The women aren't necessarily prisoners, or unwilling participants. Other options exist.
Their sexual dimorphism is not ridiculous given IRL biology (See bakker's comments on the subject on TPB).
People take their past experience and apply it to current situations, the problem is that, like here, if you have a deep understanding (say, of biology) you might see this as perfectly reasonable, but if all you've got is what you remember from high school biology a decade ago, you might think its impossible. Sometimes it works vice versa though.
Lots of TSA is about letting the story challenge you and your assumptions, science and religion included.
I'll admit I thought it seemed impossible as I read it, but I've found that it can pretty easily be explained away within the confines of Earwa Lore and/or IRL science. However, I didn't come upon the solution myself. I needed to discuss it with others.
Unfortunately, when you've got a small in-group and narrow conversation lines (ie a few active participants and one single forum thread...), the assumptions and conclusions of the few will seem to be the general consensus of the many, while simultaneously shutting down constructive conversations and abstract thinking.
Speaking broadly, for those that don't WANT there to be a possible explanation, then no amount of evidence will convince otherwise - even if an answers is served to them directly from the author. The need to be personally 'right' is more important than the story itself.
For those interested in maintaining suspension of disbelief so that they can continue to enjoy the series, suitable answers can be found. The latter being far more difficult than former.
Honestly though, for me, in the end its a fantasy series with magic and gods, space faring aliens and laser guns. Limiting what can happen in Earwa based on what's reality in present day Earth seems crazy. Why bother reading fantasy/sci-fi then? If you're interested enough, a suitable reason within the book, any book, should exist to explain whatever situation (if the book was written with care).