I'm not entirely sure, but I think the reason is the way the game's DNA system works. Inbreeding is supposed to increase the likelihood of bad traits appearing, because of similar genes (if I recall correctly, the save files show 10 genes per person, 5 from the mother and 5 taken from the father). However, people with similar traits have similar genes, so attempting to breed entirely unrelated but similar people will still be treated as inbreeding.
That's quite interesting actually. The genetic system is really well developed (and getting moreso with every facepack!)