Despite the fantastic elements of Earwa, Bakker is clearly obsessed with "rigor" with respect to his worldbuilding - however, that "rigor" seems to focus more on internal consistency than strict analogues to reality as we know it in our universe.
Some of the metaphysical (quasi-physical?) elements of Earwa just seem intended to instantiate a "Scriptural" model of the universe (e.g., sorcerers getting "salted" by Chorae, which I think Bakker has explicitly admitted).
Clearly, the Whale Mothers jangles the nerves of many readers, while other elements likely bother some more than others, depending on each reader's expertise with respect to material reality. For example, the idea that Nonmen can't parse two-dimensional images (TJE) seems completely absurd to me, but I've never read any other complaints. And there's a payoff - the alien ornamentation of the Mansions requires it, to a degree.
The explanation for why Nonmen don't commit suicide - that they effectively can't - struck me similarly as a bit of a post facto "whoops" when Bakker wanted to populate Ishteribinth with ghouls at various stages of dementia (Dolour, then the Gloom). But there's a payoff, there, too, given the centrality of Damnation to the entire narrative structure.
I suppose one could try to force analogies between the "singing" of Quyan Erratics to relatively spared musical memory in Alzheimer's patients - but is it really necessary? I'm more than willing to suspend disbelief regarding the physical instantiation of memory in human brains if that means Achamian gets to go Gnostic Wracu-hunting with Cleric.
Nevertheless, Bakker does seem at pains to justify many if not all of these fantastic elements in ways that are satisfying to
him, based on what he knows. But, as he would likely admit, he is himself blind to the Earwan divergences from the features of material reality he knows comparatively little about, and it's those storey elements that are going to bother people who know most about them IRL.
I'm guessing that there are features about the map of Earwa that annoy geologists (but I'm not a geologist/geographer, so I have not idea what those might be).
Somewhere, a structural engineer who likes dark fantasy is howling about the Medial Screw, or the Viritic Well, or the Cthonic Manse, and on and on.
That having been said, the Anasurimbor "Germ" is thought to contain Nonmen genetics (Rape of Omindalea), so I assumed that the Whale Mothers might be Wide in much the same way that Nonmen Heroes are Tall, and that Nonmen genetics support greater epigenetic lability. Or whatever.
My own problem with the Whale Mothers was that I failed to see the point - what purpose did they serve, if the Dunyain children looked like the "worldborn", instead of this:
http://vignette4.wikia.nocookie.net/memoryalpha/images/2/24/Talosians_3.jpg/revision/latest?cb=20081206044328&path-prefix=enWere the Dunyain born in litters?
It seems like the real issue is that readers suspend disbelief in the service of their own interests, and if those aren't served, they balk.
"So, you want to tell me about super-badass Thought-Dancer Monks? SOLD."
"Wait, that dude just blew up that building by yelling at it? NICE."
"Ok, there's these women...shackled...and - did you just say
shitting dogs? Um,
NOPE."