You are exactly right.
Components like to have a smooth surface. No scratches, sharp filet radius, etc. But, when you shot peen you made dents. Dents are not nice. They become locations for fatigue failure initiation. We tolerate the dents because we have the compressive layer to retard the progress of any surface dents. It is better to lap or hone the surface and remove the dented surface and make it smooth again. This practice gives you the best performance.
