A solution to level the bottom of a dado or rabbit would be to use a Stanley 71 rabbit plane. There are numerous sources for these planes: EBay, Lie Nielsen, and Lee Valley Tools to name a few. This method would be great for quick, smaller jobs.
For larger jobs (as well as small jobs) you could use a router bit that would uses the sides of the dado or rabbit to control the range of the bit. These bits come in various diameters with cutters that exactly match the diameter of the bit. Select a bit that will fit inside the dado, set the correct depth and have at it. This is very accurate and quick, and results in a very flat bottom, including the corners.
For my work, I usually always clean up any dado or rabbit with this type of router bit just to get a very clean and flat bottom.