From ArchWiki

It feels kind of funny to argue with the original author, since I wrote this one... :) Anyway, the separate plugin may be BROKEN. So if you find a fix, please tell me. --foxbunny 20:04, 25 November 2006 (EST)

Okay, so I was able to confirm that CMYK images created by separate are valid. Scribus, however, doesn't handle them well. Too bad. Kind of beats the purpose.