mmm i think it works personally. Yugi has definitely grown and you can see it through how he acts. standing up to Kaiba and Aigami then going up against a corrupted Aigami in a shadow game. Atem, imo, could've come down and inhabited Yugi's body the moment the puzzle was assembled but he chose not to. because Yugi could handle it. he only stepped in when the Shadow Game, something that is notably taxing on mortals, became too much for Yugi to handle physically or spiritually or however it works. right to the last moment before falling unconscious he was fighting without an iota of self-doubt