Can’t speak to the reasoning for Van’s desiring countersinking in 0.032” skins, but I do know that many tanks built at Synergy Air dimple the skins and aft baffle.
It does make the assembly a little more challenging with proseal and dimples, but if you can get help during this assembly step, it should be fine (and potentially a stronger assembly).
I would check with Van’s too, but I’ll be surprised if they tell you to replace the skins.