That would be a misunderstanding.
anologous to "humans evolved from chimpanzees". No, they both evolved from a common ancestor that was neither chimp nor human (or neither Bosmer nor Khajiit).
For the eyes, there's no excuse.
I disagree. Not all Bosmer had the characteristic insectoid black eyes in
Morrowind. Actually, I seem to recall it was only a minority of the available Bosmer heads that did. It is entirely reasonable to suggest that the (lore) reason Bosmer in
Oblivion don't have black eyes is that, just through random chance, none of the Bosmer NPCs you happen to meet in Cyrodiil
have black eyes.
As an anology, I know a significant proportion of German people have blue eyes. But if I go on holiday to France (where any Germans would be visitors, as Bosmer are to Cyrodiil) and all the Germans I meet happen to have brown or green eyes, that doesn't imply that something nasty has happened to all the blue-eyed Germans.
for the head it's because there's only one model per race
It would have been trivially easy to include a unique Bosmer-only hair mesh that included little horns. They did it for the Dremora.