I guess another potential reason for trading Flaherty would be a fear of him leaving as a free agent. But since that is four years away under current rules, giving up what look to be very good years ahead at a well below market salary seems a really bad idea, especially for a team not tanking, but expecting to contend each season.
Maybe it would be worth revisiting in three years from now – or sooner if free agent rules and compensation changes are enacted in the next CBA. Also, one can hope that by then, the lingering problems from 2020 will be past and the baseball labor market will settle into normalcy (whatever that will be).