The Cartmel Master Plan itself frequently ignored/rejected established facts from the Classic Series.
The original point of the Cartmel Master Plan was to make the Doctor and the Time Lords more mysterious. However, it had the opposite effect as it significantly restricted what Doctor Who could do from that point on, to say nothing of the fact that it told us exactly what and who the Doctor was.
The New Series was also not the first medium to reject the Cartmel Master Plan. The TV Movie explicitly mentions the Doctor's mother(as an example). The BBC Novels, DWM Comics, Big Finish Audios etc. Had similarly all chosen not to incorporate the Cartmel Master Plan(and indeed many of the other Virgin books revelations) into their backstory.
The BBC is also bound by a Charter that means it can not assume that viewers of the television series have watched/read/listened to spin-off media. Had the New Series wanted to incorporate the Cartmel Master Plan into its continuity, they would have had to fully (re)introduce.
In the end, the Cartmel Master Plan was simply too limiting and definitive. Far from expanding the Doctor Who mythos, it restricted it. The Virgin Books also gave numerous characters backstories, real names and final fates. Again, far from enlarging Doctor Who, it shrunk the possibilities for future stories.