Since nobody else answered:
As I recall you match drill the flap fairings to those holes. If you dimple them first it makes it harder to accurately match the location of the hole. I did them with the Cleveland pop rivet dimpler later when installing the fairings. You see that feature every time you get in the plane. Could you dimple them first? Sure. It’s the same as someone needing to replace a non pre-drilled skin on an existing part.