Frustrating to see nearly a year later and we’re still having these same flatness issues: Carriage Tolerances - Unusable Over Distance >75mm From Center
I got support to send me a new carriage and the new one was actually worse than my current one, and 1.2mm deflection.
@Thick8 machined each boss in situ. I am planning on doing something like that as well.
Shims are also used, installing aluminum tape (in @Thick8’s case) or pieces of post it notes (in my case) where needed to being the mounting surface up to level.
Another thing that can be done is either mill the wasteboard (in @sdj544’s case) or a sacrificial board (@WilliamBosacker’s recommendation) flat using the machine to generate a level surface without modifying the underlying carriage.
Make sure you have pushed the X axis all the way to the top or have some other way of repeatedly tramming it so that you don’t lose the level surface if the machine skips steps on just 1 Z axis.