Self-intersection is not the same as cutting. The disconnect you’re experiencing is between the mathematical description of the problem—-does there exist a smooth homotopy of immersions between two embedding a of the 2-sphere in 3-dimensional space—and the colloquial description. The mathematical phenomenon corresponding to cutting would be discontinuity of that homotopy, which is different from the description of self-intersection, which amounts to the difference between an embedding and an immersion.