Hypothesis: Khajiit solidarity and identity is not a fixed thing, nor does it always react in the same way to external forces. In response to the heavy hand of the Third Cyrodilic Empire, Khajiit drew together. In response to the Interregnum-time Aldmeri dominion, Khajiit become more factional and less trustful of their own kin, especially in the decades following the death of the the Riddle-Thar.
The effects thereof: Senche-raht exist in the second era, but are not considered true catfolk. They are sub-feline, produced of the furstock, but not a child of the sands in the same way as other creatures a litter-mother might produce. They are not the only exception to this rule: that is why there are, according to the Moon Bishop, only seventeen true breeds of Khajiit, which do not vary in height quite so much as the others (Alfiq are in, Sench-Raht are out). The others are either misnomers or accidents.
Moon Bishop Hunal is in this respect dated in his views: the "lower" castes of Elsweyr are becoming gradually recognized (and indeed eventually the caste system will be forgotten altogether).
A very hazy and easily dispelled proposal, but it conveniently fixes this one specific thing.