You can certainly make new MDF inserts (or out of other materials as some members have elected to do). Someone modeled some up here 3D model of the Shapeoko Pro wasteboard - #8 by mickeybob, and I think there are other files/info located elsewhere.
I personally haven’t yet surfaced my slats on the 4. If I need a super flat surface I’ll bust out a piece of MDF and attach that then surface that piece. I hop around projects quite a bit, so if you have consistent work, it may be helpful to do something that helps facilitate that.