No explanation is possible. A number of locations exist in one but not the other. I guess the only possible reason is that Nchardak was submerged, but eventually returned to the surface, but I think that sounds ridiculous.
2601:155:8401:F8E0:C0B1:29EF:80E1:A6D5 wrote: Yeah you're right. A dwemer ruin being able to go above and below the water? Absolutely ridiculous. Who could honestly believe such a thing in the world of Elder Scrolls?
What's funny is that Nchardak is said in Skyrim to be rumored to be able to submerge and reemerge from the water, so I think our detectives just figured this out. Case closed. ;)