The inserts are for the investigator and shoggoth miniatures. Probably for people wanting to paint them and keep them from shaking around in the box. Idk about any expansions, but I'd be cool with them!
I agree this is what they are for, however people who are going to spend the time to paint the minis are also the ones who are going to sleeve the cards; and there is no room in the box for sleeved cards without throwing the insert out.
It's a really bad design.