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.

I'm not sure what sense you're using "the same" in. Eg a cylinder can be transformed into a mobius strip (in 3d space) by cutting and gluing, but if we allow only self-intersection, this can't be done. To me this shows that they're not "the same".