Make the physical meta physical and you have your answer.
The dunyain belief in the principles that underlie their training are delusions. We--the readers--think the Dunyain are accurate and not deluded, because the dunyain are using scientific principles and explanations we ourselves recognize, therefore we are as deluded as the Dunyain.
The reason those principles are delusions is because the Dunyain have discarded information of the metaphysical and so all their conclusions follow from an incomplete data set. And the metaphysical is crucial to understanding what is going on with their abilities.
So if the Dunyain lived in our world, they would be exactly right, because in our world there is no metaphysical data to include, and infact including such data in scientific study would corrupt the validity of scientific conclusions.
But this means in a world like Earwa, the Dunyain are exactly wrong, because discarding metaphysical data means you can never get a correct conclusion.
So what does this mean? We see with Serwe's Heart (where her and his soul are so close that Kellhus can grab her heart via his own chest, the heart being the seat of the soul) that souls are connected. Kellhus and Achamian later explain that each soul is like a pinprick of a greater light. We see both Esmenet and Serwe and Cnaiur have all acquired 'leaky' information from Kellhus or Moenghus via the closeness of their mundane souls to the Dunyain souls (Esmenet has out of body experiences, seeing herself from Kellhus' or Serwe's eyes and also picks up lots of Dunyain terminology like Absolute that Kellhus rarely ever vocalizes (but thinks about regularly). In other words souls are connected and communication happens from soul to soul, incredibly fast.
Just like how the thought that causes a face to smile happens incredibly fast, the thought leads to the action of smiling, and Kellhus and the Dunyain think that they see the muscles reflect the thought, they think they reverse engineer the muscle movement to identify or hypothesize the sourcing thought.
That would be right, in our world. Technology is being worked on that analyzes the muscles of the face and tailors advertising based on the reverse engineered hypothesis of what thoughts (conscious or unconscious) caused those muscle movements.
But we know it's not right in Earwa. What's happening in Earwa is something the Dunyain cannot conceive--so because they cannot conceive it they have invented an elaborate belief and training structure to explain it: they read faces.
What the Dunyain do not realize is the metaphysical component. They are not reading thoughts from faces, they are reading thoughts from that super-fast soul-to-soul communication. Their training and breeding would still select and hone this ability, they just wouldn't understand the origins of what they are doing, because they think faces not souls. This is why the native ability is metaphysical--based on the proportions of the soul in question--rather than genetic. So Kellhus' children have a lot of his abilities because of the proportions of their souls, not because they were trained as he was. They lack the technique but they have the talent.