Hey Mark,
usually the wasteboard slats are much thicker than the T-slots height.
Although the idea to have T-Slots flush with the MDF would be nice, in order to use Veritas Bench Blades for T-Track.
Milling the MDF slats flush with the T-Tracks when they are mounted is nothing I would do. I would mill the slats before you assemble them into the tabletop / QCW Frame.
However I would not object if you trust the accuracy of your machine and your g-code program, and your bit length / Z probing, when doing such a milling job. And that the bit diameter really corresponds to the specs.
Be sure that your machine base is properly rectangular (“squared”) (bar gauge) and coplanar (“not twisted”) (fishing line method) and that your Z mount / milling motor / spindle with the bit is absolutely perpendicular to the (squared and untwisted) machine base / table top / QCW frame.