I powder coated my panel and it adds quite a bit of material.
I did not countersink my panel because I like the look of black button head screws on the panel, so I can't say from personal experience how much the powder coating will fill the countersinks .... however, the powder coat added enough thickness that I needed to carefully file the edges of the panel pieces to get them to seat properly with one another and the upper fuselage skin.
So based on my experience, I would plan on countersinking at least a couple of clicks deeper ... or better yet, make a test strip of aluminum the same thickness as the panel with an assortment of countersinks made to different depths. Take your test strip to the vendor you plan to use and have them powder coat the strip using the color you are going with and see which countersink yields the finished look that suits you.
RV-12 Wings, Empennage, Fuselage, Finishing, Avionics and Powerplant kits all completed
Dues paid until September 2019