There is a 1% chance that Boone does not come back. I'm almost certain there is an end of season meeting between the manager and GM. I'd imagine Boone's performance will be reviewed and they'll touch on the areas where they feel he can improve, most notably when to manage by feel vs when to manage by the analytics. He's a rookie manager so it's not like he can't improve. And despite some boneheaded moves this year, he was probably the second best rookie manager this season behind Cora. And Cora had experience coaching other aspects of a team so he wasn't as green as Boone.
If I had to grade Boone's management for the ENTIRE season in my most unbiased attempt, I'd give him a C+.. maybe B-.