Creating small flat bottom holes in plastic models for magnets
I can't answer the specific question on drill bit types.  I've don plenty of magnatizing, but haven't analyzed the tools I've used in that great of depth.

I've used Dremel's precision drill bit set in my 7.2 Volt rotary tool.  I've never had too big a problem with the convex bottom of the hole they create.  If you match the drill bit size close enough to the magnet diameter, the sides of the hole should provide enough surface area to hold the magnet in place with a little super glue.

A little super glue, epoxy glue, or an epoxy resin like Green Stuff or Milliput could be used to fill in the hole to an even surface.