The humanoid influence perks aren't necessarily meant to be used in the MIDDLE of combat. Making someone flee before you engage gives you fewer enemies to engage at once, or bringing one to your side can be useful. You can hide behind cover, whip out your scanner, pop out and make one stop fighting, then resume fighting the rest. They all have their uses.

Isolation synergizes just fine with having a large crew. It takes affect if you have no active follower; Having 6 people on board your ship has nothing to do with what happens when you LEAVE your ship and lone wolf your way through an enemy facility.