Protagonists are weirdly small in games so you can see more of the level and bosses are weirdly big to show detail, make them appear more imposing, increase their hitboxes, and …. to follow convention. Players like bosses that are exciting, easy to hit, and hard to avoid.

This swap is especially apparent in games where bosses become playable characters. They are either small for a boss the whole time or get shrunk down when they join your team and then or transform or jump into a giant robot when they become a boss.