When I want to drill a flat bottomed hole I use a center cutting, end milling cutter. They will leave a very slight convex bottom (the center will be just a few thousandths higher), but for most purposes it will be flat. You will need a rigid set-up because there is no centering action with these milling cutters as a normal twist drill will have. You could probably do it on a good drill press with a vise bolted down, in place, but a milling machine would be better.
When I want to create a counterbore for a bolt, like a socket head cap screw, I use a DeWalt style bullet drill for the first operation at the hole's location and follow up with a body sized drill or whatever smaller size is needed. Again, the edges will drill just a bit deeper than the area closer to the center, but for most purposes it is OK. And SHCSs fit just fine. They are a LOT less expensive than proper counterbores. Again, the trick is to bore the larger, counterbore FIRST, not afterwards like with an actual counterbore. I have done this many times and the result is always satisfactory. I have an index of these bullet style drills that I mainly use for this purpose. I have also slightly rounded the outer corners of these drills to produce a small radius at the inside corner of the counterbores. I think this reduces the stress at that point as a sharp corner is usually a stress riser. I used a hand stone to do this.
If you need a truly flat bottom, then the less expensive way is with a boring bar. If you do that a lot, consider getting a boring head. Of course, this does not work well for real small holes.
You could also make some gun drills.
