I'd guess these give you flexibility, air-cushioning in case of a drop and also save some weight and material as they are hollowed out. The «hole» might also serve as a place to park the pencil while using it for a moment (not sure if that actually works from the images).
The circular hole is to place your pencil in, so it's upright & ready when you are using it.
The corner holes are for shock absorption, in case you drop your iPad.
The extra space at either end of the pencil is to allow for you to take the pencil out of it's holding area. Sometimes cases come with a hole in the middle of that holding area on the bottom, so you can poke your finger thru and push the pencil out. If your case doesn't have that, they will allow extra space at both ends of the iPad for easier access.