Is there any in-universe explanation for this change from the way the universe seemed to be in Civil War?
Não ...
Nós simplesmente não temos nenhuma informação sobre porque Pepper e Tony estão juntos novamente. Eles apenas parecem estar felizes novamente.
Tudo o que sabemos é que eles estavam "em um intervalo" durante Guerra Civil porque os produtores / diretores queriam que Tony estivesse "fora de equilíbrio" para aquele filme.
"The intent in this movie, because we knew where we were going with the character, [was] that we had to motivate Tony to want to kill Bucky Barnes in the third act in order for the third act to work correctly, that Tony would have to be off-balance," explains Russo.
"The way that we thought we could make him off-balance was by pulling things out of his life, making him emotionally vulnerable. Really emotionally vulnerable," he continues. "So, Pepper is out of his life. It clearly is an issue for him, as you can see, by Robert's performance here."
In Civil War, Tony told Cap that he and Pepper were on a "break" because she felt he was too obsessed with his work as Iron Man. He hoped that signing the Sokovia Accords would be a good compromise and help keep him in line for her. It's unclear whether or not Pepper is actually in favor of the Accords, though given the final act of Civil War, it would be surprising if Tony himself were still totally on board.
Presumivelmente, as razões do universo para a ausência de Pepper não se aplicam mais (ou ela apenas encolheu os ombros e o perdoou).