@SandFish - I assume your referring to this dialogue
1. I can't answer this definitively, but I would guess the covers would be generated according to the current setting in Generate Cover customisation, viz :
3. I would assume the Clone covers is there because someone asked for it. Some users have multiple instances of the same book (different editions, languages, translators, illustrators etc) - they might like to have all instances use the same cover.
BR