The side-quest is actually its own plotline distinct from the main story "routes" (though not entirely independent given some of the objective requirements.) The condition for the third branch is still related to the fate optional party member, as there is one more state for them beyond recruited or not.
And yeah, I get you. Honestly, the inflexibility of the controls is something that annoys me a bit, too. The benefits of the engine definitely outweigh that annoyance for me, but I do want to keep looking for possible ways to make them a little more comfortable.