Actually, Nobodies are still very much a different sort of person in the case of Roxas and Naminé due to how they were created. Sora temporarily loses his heart and creates Roxas (and Naminé since Kairi's heart was inside him at the time). But he and Kairi soon afterward regain themselves, yet somehow their Nobodies still exist/co-exist with their existences. Roxas and Naminé end up starting out as blank slates though instead of having the memories of their Others. And depending on their canon point, they can have a good handful of their own memories (In Roxas' case, he might remember bits and pieces of Sora's memories, but he isn't attached to them/considers them his memories). Naminé admittedly knows more about Sora and Kairi because of her power, but in the end, she's very much her own person.

Otherwise, usually Nobodies and Somebodies don't co-exist in canon anyway because they are their Nobodies. A Nobody is just basically their bodies and memories ie. Axel, Saix, Vexen, etc. They were all fully Nobodied, persay. That's the best way I can explain it. So, I could see like... not allowing both Isa and Saix to both be in the game. But those like Sora and Roxas or Naminé and Kairi, since they both co-existed in canon, it's a little different, I think.

And it's alright. Kingdom Hearts is one of those series that even I can kind of struggle to explain here and there and I've roleplayed from the series for a while now.