There are 3 years in between the end of Into Darkness and Beyond - aside from what happened in the comics, surely there are things a novel can be written about. And there's a whole year in between Kirk's Khan blood resurrection and the Enterprise repairs. Don't tell me Starfleet kept the entire senior staff on ice for a year. Spock may have taken a 6 month posting somewhere; Uhura may have joined a particular contact mission due to her language expertise.
For that matter, the Teenaxi debacle was Kirk's last straw, the last incident prior to him considering a desk job as vice admiral. What were some of the prior straws? Treklit has books that show events which culminate in Spock Prime's decision to undertake kolinahr, so why not this?
What was Spock Prime doing when not meeting with young Spock?