HMMM. IME, a slightly oversized drill, if the part is held in a drillpress vise, because it WILL tend to
be grabby and the vise is held but permitted to be free to move slighty laterally, will self center very well. And
the hole bottom not being flat, should not be an issue, the outer perimeter if the screw should hold it
down fine.
If you drill it up, partial depth, don't "unflatten" the bottom of the counterbore, then use a mill cutter, which
will now fit in, not touch the sides, you can then deepen the counterbore and maintain a flat bottom.
I will add that I have not done this on a receiver site, but have on other, similar items.
Bill