If you claim a threesome then the threesome has to be in the fic, however all three *characters* do not. Does that make sense? You can't write about two of them and just ignore the third person, but they don't all have to be physically present in every scene. They don't even all have to have got together for every scene - in another challenge I have a couple becoming a threesome and they're not technically a threesome until the third of fourth fic, but the 'threesome' is a part of each fic even if it's only two of them discussing the idea of the third character.
I'm not sure how clear that is at all, lol. Basically yes you can play around with the dynamics and aspects of the relationship as long as you don't ignore 1/3 of the threesome all together.