Mike, I accidentally did the same thing. When the countersunk hole is not knife-edged (countersink depth extending all the way through the part), a countersunk fastener is actually stronger in shear than an equivalent-sized universal-head (AN470) fastener. This is because the joint actually sees a little benefit from the average fastener area being increased.
In tension, the countersunk fastener would not fare as well as the universal-head fastener. But this is a shear application, and tension is not normally the critical loading condition for rivets on our RVs.
The thickness of the doubler makes this absolutely nothing to worry about. In fact, you're exactly right about your "mistake gone good" comment. You did the structure a favor by countersinking.
Not sure I'd continue to deviate from plans for 100% of the rivets there, however, but only for the simple reason that I found it no problem to buck the skin rivets with my small tungsten bucking bar. If you don't have one of those yet, you'll be amazed when you try one.