Hey Paul,
if you do it “for stiffness” like they say in the manual, then it’s clearly the wrong way to add stiffness to your table top. A wasteboard is made of MDF and MDF is not good for stiffness, and you don’t use your wasteboard to add stiffness to your machine bed. A thickness of 2.5 - 3" inch is perhaps necessary (or perhaps not even sufficient) if you want to build a table top made of MDF, but I would not recommend to build a table top of MDF as it’s not stiff, heavy, expensive, and fears humidity. While it’s ideal for wasteboards, an anti-torsion box made of 12 mm birch plywood is much more stable as table top (search for “torsion box” to see examples in this forum).
Generally, if you stack wasteboards on top of the other, you give away usable Z travel of your machine. On Z-16 assembly, you have 133 mm usable travel. You have three mounting positions of the Z-16 assembly so you can lower it to drill through, or mill into, your wasteboard or even table top (see pictures below). I find it more logical to lower the position of the Z assembly to drill the initial holes into your wasteboard, and to use the middle or higher position for normal use. In practice, for future new wasteboards, you could omit the step of lowering your Z assembly because you could put the new wasteboard or wasteboard slats on top of the old “wasted” wasteboard, drill your holes, and then replace the old wasteboard with the new wasteboard.
PS: Z-20 assembly as found on Elite Series has four mounting holes and 160 mm travel, but the same applies.
PS2: Is your machine base the QCW Frame?
Welcome to the forum!