When it comes to the ceremonial duel, do you think Atem "decided" to go to the afterlife for himself or was it for the sake of Yugi's confidence and independence?
For the rest of my answer:
We don’t know what Atem would choose if the choice was completely free because the manga never shows us Atem’s thoughts and it’s something that never gets discussed. When both Yugi and Atem talk about the ceremonial duel it’s always in terms of what they see as their responsibility to their partner. Both are acting out of a pure, selfless love for the other. Yugi wants to win because he sees it as his responsibility to help Atem reach the afterlife. Atem is willing to follow whatever the duel decrees – if Yugi proves that he is strong enough to stand alone, Atem will leave, if not he will stay.
I like it that we don’t know what Atem’s own dreams and wishes might be, because that emphasizes two very important things about Atem. As a Pharoah, he was willing to protect his people at the cost of his life. As a spirit he came to life to protect Yugi and always lived up to that mission. Atem feels guilty when Jounouchi is in a coma at Alcatraz because he blames himself for pursuing his own identity, believing it led to Jounouchi’s condition. Think of that: Atem feels guilty for wanting so basic as an identity and memories. I think Atem doesn’t consider his own desires because he doesn’t know how to even frame those thoughts into words and possibly doesn’t feel that he has the right to them anyway.
Atem believes very strongly that duels exist to test beliefs and that they are guides to future actions. So it seems entirely fitting that he would believe that it was proper for a duel to decide his fate and not to question it further.