I actually don't mind splitting them up, per se, as you're right, it can show the Companion's agency (which is a lot of what I love about Martha and Nyssa -- they separate from the Doctor and accomplish awesome on their own).

With Gatiss, though, I feel like he separates the Companion to 'get them out of the way'. They are almost barely a big part of the story and often it is people around them that have to come to their rescue or make them awesome, they are not just awesome on their own. Like they 'need the mens' to help them because they are not strong people on their own.