Hey John. My first thought is that there are a lot of makers that have this figured out; you will too. Second thought is that aluminum pins are relatively rare on handmade knives in my experience. I personally dont care for the color/look of Al in finished work and a frequent comment is that the stuff work hardens so fast on peening that it can be miserable to get right.
I use 416SS mostly, but also 304SS, nickel silver and occasionally brass pins. All are harder than most common handle materials and benefit from a similar approach towards keeping them flush through finishing process.
To expand on what Bill said, my personal process goes something like this. Shape handle to about 95% nominal and pin. Peen heads till lateral movement stops. Give epoxy seal time to set up properly then file off heads and continue to work the handle to final form.
Now that pins are cut down dead flush and handle is in final shape
so the trick is to maintain that flush geometry till polish.
A sharp 6 or 8 mill file used in a draw/push filing motion will help keep things flat as you go along, but once the sanding starts, stick with fresh sharp abrasives combined with a backer of the appropriate hardness and you can likely avoid going back to the files again (I also selectively use fine and medium diamond files to go back and knock down proud heads with minimal damage to surrounding finish).
To state the obvious, what is causing the problem is the removal of surrounding handle material at a faster rate than the pin material. The idea here is that hard and flat abrasive backings simply do not allow this, especially if you can span two or more pins on contact of a single stroke. Change to fresh paper often, use light pressure if possible (maybe back up a grit or two instead), use a hard and dead flat backer (I prefer diemakers stones because, even bone dry, the paper doesnt slide easily like on steel backers). And have an orderly plan for finishing (e.g. mill file, 220, 320, 500, and 800 grit etc).
With a plan in place, dont move up to the next grit until you have your best work done with the previous one. Look as much as you sand. Check flush as you go and dont let it get away from you. For the final few strokes at high grit, you can get away with a softer leather or rubber backer, but each stroke will take you (slowly) in the wrong direction. Geometric form (pins being flush) must take precedence over surface finish till the end and you can have both very well done approaching it this way.
Good luck to you and hope this helps.