Assuming your rails are strong enough to not sag as the motor and cutter move along the length of this—
Let the tool flatten its own base.
Install a wide bit, sometimes called a surfacing bit or a spoil board cutting bit (your sacrificial base is called a spoil board) and set a program that sends the router over the entire base, taking a very light cut. You may need to do this additional times.
A top of MDF will machine smoothly, but it creates a lot of fine dust. If the irregularities are severe, use 3/4” thick material as the base, and you can resurface this many times. 1/2” thick MDF will be less expensive, though.
Here is one which uses replaceable carbide inserts for its cutting edges. There are less expensive versions made of high speed steel, or carbide tipped, which are resharpenable.
This should cut away all the high spots and leave you with a flat base.
Paul Jacobson