I have a bunch of test pieces, made from all the thicknesses of skin, with properly sized holes (#40 and #30) and then dimpled for 426-3 and -4 rivets. I use this, as appropriate, to set the size of the countersink correctly...the dimpled skin must fit inside the countersink.
BTW, if you haven't done so, countersink and rivet in the nutplates (I think it even says so in the instructions), to keep the countersink pilot from wandering...you'll end up with a hole on the "inside" of the countersink that is a bit larger than a normal drilled and dimpled hole, IIRC.
Bottom line...make some test pieces and check for fit.
Steve "Flying Scotsman"
Santa Clarita, CA
PP-ASEL, ASES, Instrument Airplane
RV-7A N660WS flying!