A short explanation is that a good way to classify certain three dimensional shapes is by the number of holes they have. Since the number of holes doesn't change if you change the shape in certain ways.
So all the shapes that sensei has made are in some sense the same since they each have one hole in them.
I'm omitting a lot of detail (like, practically all of it) here, if you want to know more, look up the classification of compact closed surfaces.
The little bar thing she ate on page 11 looked like the same rations Yuu and Chii found in the plane in Girls' Last Tour. Idk if it's actually a reference but there's been plenty of other references to the author's previous work in this so ya know.
@Serenata has homed-in on an important point. Topologically speaking, the hole-digging club has not yet created a hole. However, by making a u-turn, to create a tunnel from one part of the school grounds to another, they can do just that. There is no need to tunnel straight down.