I think that was true when Gary Russell was running the ship, but that changed I think when GR left and Nicholas Briggs became exec. The Company of Friends exists so as for BF to say "look, McGann's Doctor did have adventures with all other companions!" and its a novel approach... but from what I read, the novel series is starkly unique in a way the audios and comics aren't from the show as it returned. I gather the book range never concluded things, but I can imagine only a history rewrite would be a satisfactory ending would suffice in order for it to sit with the audios.
Lance Parkin's The Gallifrey Chronicles is a conclusion, in the way that "All Good Things..." is a conclusion to Star Trek: The Next Generation -- this era of the adventures end, there's a resolution to various dangling issues, but the adventures themselves don't end.
The Gallifrey Chronicles actually jokes about the different and contradictory threads of the eighth Doctor's life, as one of the characters looks in a Time-Space Visualizer and sees that the eighth Doctor has three different ninth incarnations (Atkinson, REG, and, at the time, Eccleston).
There have been a number of different ways of fitting the different threads together proposed over the years -- fitting years of adventures into the middle of Sam Jones' Greenpeace festival has long been a popular kludge -- but I don't think I need to know anymore how the pieces slot together.