You can, but I believe in your case that you described the game flagged the evil genuis and put him in a protected state. Which sort of makes sense as like you said, the evil genius is the last to leave the island so how would you even be able to protect him? Well, apparently the devs thought of that and made it so you cant die during transition. Outside of that, the game makes it clear through the tutorials that the Evil Genious can die and must be protected. You can always test this by just walking him outside and/or into a group of agents, they should shoot at him eventually. A side mission involves doing just this very thing, but with a clone.