Nothing in The Timeless Children actually contradicts what either TV series has told us about The Doctor's childhood. It was always vague and opaque. It was the 7th and 8th Doctor novels that actually went in-depth about it. Hell, we've even seen Time Lords change age after regenerating. There's nothing keeping the first Doctor of the latest post-mind wipe cycle (Hartnell's Doctor) from initially regenerating into a child. The child who slept in The Eleventh Doctor's cradle. The child seen in Listen. The child who grew up alongside The Master. A fuck ton of the Wilderness Era Whoniverse just became an alternate Whoniverse. Which works surprisingly well with both Zagreus's visions of alternate timelines and At Childhood's End recent creation of alternate timelines in 1990 shortly after the Classic Series ended. Liz Sladen's Big Finish audio series Sarah Jane Smith fits neatly back into continuity now. It's just part of the 7th & 8th Doctor novel/Bernice Summerfield/Faction Paradox universe. Also, the "Ground Zero" debacle is solved. That wasn't the mainline continuity Ace (Classic Who, Big Finish, Gallifrey, Sarah Jane Adventures reference, At Childhood's End). That was the novel version of Ace that split off shortly after the Classic Series (Classic Who, Virgin New Adventures, Doctor Who Magazine strips, The New Adventures of Bernice Summerfield). Which means only the 7th Doctor strips are part of this continuity. As is half of The Company of Friends: "Benny's Story" and "Fitz's Story". As is The Worlds of Big Finish crossover event. Basically, anything with Benny in it is now part of that continuity. The Eighth of March and The Legacy of Time now work as brief glimpses of that universe's NuWho era world. As for Braxiatel and Iris Wildthyme's appearances in both continuities? Well, their timelines were always delightfully convoluted anyway. Iris has always been heavily hinted to come from another universe (The Obverse, not the alt-Whoniverse I'm now proposing). And at least some of Braxiatel's appearances have been implied to be a Brax from another universe. Universe hopping seems to come quite naturally to them. The only remaining continuity conflict is Benny's brief appearance in an episode of Gallifrey.