Real talk as I exspected Shigeru remembers but he cannot communicate it properly since he's still in recovery. This also confirms that they both saw butterflies, so I'm guessing that rules out the Seiichi psychosis theory.
But back to the breakfast question. In the beginning when things were normal (normal for them at least), Seiko would ask Sei if he wanted a meat bun, or bean bun, and Sei would always choose meat bun. As controlling as Sei was she allowed him this one freedom, this illusion of autonomy. So that Sei would always believe that she cared about what he thought. And listened to what he had to say.
But when they had their falling out (i.e. Seiko literally strangling her son for confronting her on what SHE SAID), she stripped him of his one choice and instead told him what he was going to eat.
But now we can see the "affectionate" question is back, but instead of leaving Sei the illusion of choice, it leaves us the audience with illusion of normalcy. It's easy to take this as a sign that everything is back to normal in their home, but there are key differences that show thing have irreversibly changed. This time when Seiko asks instead of picking one, Sei says "either is fine" representing how he has given himself fully to his mother. And honestly could you blame him after all the abuse he feels he has no other choice but to be her molding clay. But for me it's Seiko's response that's trully the cherry on top. She chooses a bean bun. Even tho when given the choice Sei always chose a meat bun, she chose a bean bun for him instead, and I believe this is her way of communicating that she is the one fully I control, they will now due whatever she's planning to do, and Sei is ready to happily go along.