Trivia: Clara's cameo was originally intended to be slightly longer, with her appearing on screen with the Doctor, Bill and Nardole. The three Companions were going to ask the Doctor which one of them was his favourite, and he was going to evade the question. Clara's brief, vision-like appearance came about because Jenna Coleman was too busy working on Victoria to shoot that version of the scene. She shot the scene in an office in London, with the background CGI-ed in.
Trivia: The planet where the Doctor goes to see Rusty is Villengard, which was famously mentioned in "The Doctor Dances" as where Jack got his sonic blaster from a factory that the Ninth Doctor later blew up and arranged to replace with a banana grove.
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.