I think I've found something out about that.

The staple seems to deflect in-plane (the plane the staple would lie in if you put it on a table). They almost never deflect out of plane. What I'm trying to describe is that they curl their ends like a cotter pin - the legs don't stay parallel and curve like railroad tracks following a "U" shape.

If you align the staple so that the plane of the staple is in the plane of the work, all the deflection stays within the work - no ends poking out.

The last four boxes I just built didn't have a single one poking out except when I forgot to change out for shorter staples and they went clear through :-^