imagine if the companions multi class /subclass options were changeable by in game quests
some examples;
Xoti you can alter her faith through quests or dialogue choccies which influence her faith. potentially priest/monk subclass.
Helping/encouraging Serafen to be more focused and centered you can remove/alter the wild element of his cypher abilities
perhaps you can complete a quest that leads to Tekehu realising he can also sing unlocking the chanter multiclass.
an alternative to unlocking them over time might be to have the watcher see a vision from the companions past. and making a choice at a key point could influence the choice.
example:
when meeting Eder your watcher abilities kick in and you see a choice Eder makes during the 5 year gap that leads him to multiclassing as a rogue or staying a pure fighter.