OH BOY. FINALLY, A TREND THAT LETS ME PUSH MY CLOSET MARIOxBOWSER PAIRING.
Well, since this is technically a Sunshine pic, I might as well put my dumb fan theory here. Maybe it's been suggested before, who knows.
Back at the end of Sunshine, when Bowser told Bowser Jr. that Peach was his mother, he wasn't technically lying. He just phrased it in a vague way due to embarrassment. While Princess Peach herself isn't the mother, Bowser as Peach, I.E. Bowsette is, and Mario is the father. That's why whenever Bowser Jr. puts on his mask, he transforms into Shadow Mario as a reflection of his actual father's image.
Perhaps the real Peach's confused reaction was mainly one of ultra sheltered ignorance of the "How is babby formed" variety.
whew. Glad I got that out of my system.