Terraphiles was being written at the time when Moffat would have had an outline for season 6, and was intending to use Jack in A Good Man Goes to War, and because of that, Jack wasn't allowed to be used in Terraphiles. Similar thing with the Twelfth Doctor book with Bernice Summerfield. The original plan was to use River instead, but Moffat was already writing The Husbands of River Son which made her off-limits for that book. Hell, even RTD had a short story planned for 2013 which was supposed to be about the end of the Time War and the Eighth Doctor's regeneration which had to be abandoned because of Day of the Doctor, though that at least did see a release as Lockdown Bonus Material earlier this year.
The novel with Ace meeting the Thirteenth Doctor, as well as all the stuff you mentioned in the audios only happened because there are no plans for them to be done on the show. Part of the approval process tie-in materials go through is to make sure they aren't covering material that is being planned for the show.
