Hmm, my Kindle 11 emanates no light whatsoever on its lowest setting (I've a pitch black room) but my brain still can't deal with it. Same issue with the Boox. No light emanated on the lowest setting but headachey nonetheless.
In contrast, the Kindle 4, which has no light function per se, feels fine.
To sum up it appears to be the presence of a light function, whether activated or not (the inactive function might still be active in the sense that it has a bearing on the perceptible stuff), that my brain doesn't like.