You are misreading the document. The muons are created in the top of the atmosphere and decays after a very short amount of time. The point is that they decay so fast that they shouldn't be able to reach the ground. They manage to do that because time passes much slower for the muon. Or to put it differently, from the point of view of the muon the thickness of the atmosphere has been compressed to become much smaller than from the point of view of an observer on Earth.