Whenever I dimpled both the top and bottom items with the same dimple die, it looked like there was an ever-so-slight gap between the aluminum parts. This was easily observable where two edges came together.
My solution was to use the "tank" dimples on the lower part and "normal" dimples on the top part. This allowed the parts to nest nicely...IMO.
Recently, there was a link to a "how to dimple" animation (I think produced by Disney's studios for the WWII build efforts). This showed that each succeeding layer of aluminum gets a slightly different dimple geometry so that all parts can nest properly. In effect, this is what the tank dimple dies and normal dimple dies accomplish.
In your case, I would not change anything. Leave it the way it is. But if it really bothers your sense of aesthetics, then leave the tank dimples on the ribs and only change the skin dimples to the "normal' variety.
As an aside, some number of years ago I attended the Oregon State EAA convention. There was an RV-6 there that I sworn had composit wings...they were that smooth. The owner/builder/pilot stated that he purposely dimpled the wing skins slightly deep. He thinned down some pro-seal and dabbed it onto each rivet head, and smoothed it down to the skin surface. After painting, the rivet lines completely disappeared. The wing was truly as smooth as glass.