Bosmer don't seem to have surnames, except royalty. He could be another member of the family, but since he's described as Camoran Kaltos' advisor rather than a relative, I think it's more likely that he either claimed the title for himself or was adopted like the Romans often did. I don't know why Kaltos has a surname-forename structure when Haymon and Mankar have a forename-surname structure, though.
Another possibility: I got the impression that perhaps, since the family is so old and perhaps more genetically 'pure,' they are close to the original aldmer stock, like the chimer, ayleids, and presumably altmer.
The real reason is almost certainly that the designers felt a Bosmer as the game's main villain was not very imposing. I think they're pretty creepy in their own way, though.
Edit: And, correct me if I'm wrong, because it's always hard to tell in TES, but the Refugees was supposed to be historical fiction, wasn't it? If it's a novel or whatever it may be complete BS, have a kernel of truth, or be based on the author's thorough research. It's hard to say.
Yes, i thought it was strange, too, that Camoran Kaltos has the structure of his surname different from the other named family members... And you are right about many of your other points, too. So, I guess, since it's not really specified in lore, I can just make it fit however I choose for my story. Probably best that way, anyway.
Personally I believe that ever since TES III the Bosmer became somewhat of a joke, which continued in TES IV. I'm hoping Skyrim doesnt do them wrong, and we get to see a somewhat grimmer side to them.
Grimmer side of Bosmer would be nice to see in Skyrim. But if you want to see Bosmeri who are not a big joke, and if you like fan fiction... *begin advertisemant* ...you should read my fan fic, linked in my signature. It has very grim and dark nature, of course, because it takes place in a very dark world. If you didn't like SI and Bosmer in TES IV, I can assure you that I paint a much better, darker and more in depth picture of them in my SI fan fiction. I highly recommend that you check it out.
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;)