The Return of Doctor Mysterio - S10-E1
The Doctor: [Looking at the Superman comic] Take a look at that picture.
Young Grant: OK.
The Doctor: Now, this one. Take a good, long look. Takes a moment to see it.
Young Grant: See what?
The Doctor: Superman and Clark Kent are one and the same person.
Young Grant: Are you serious?
The Doctor: Yeah. Look, I drew specs on Superman.
Young Grant: Everyone knows they're the same person.
The Doctor: Uh. Well, Lois Lane doesn't. And she's a reporter.
Chosen answer: 1) When Stephen Moffat took over he ignored a lot of what had been developed before (there is not in-universe answer). 2) It would have killed Rose, so the Doctor absorbed the energy. His body regenerated before the energy could do a significant amount of damage that would prevent regeneration.