Upload & Sell: On
This has nothing to do with the flatness, and we are not talking the precising mechanic here
There are three paths the light goes into your camera: A: sensor, B: AF module, C:Focus screen to your eye.
Once distance A=B and A=C, you are fine. If not you need adjust.
If A=B mess up, you need micoadjust your body. If A=C mess up, you need adjust your screen.
If your screen tilt or AF module tilt because of manufacture tolerance, you need adjust those screw, but most likely, Nikon has done that before units are for sale. As I said, unless that is verified, I won't do that.
Your D90 screen has different thickness than Katz, thus the problem.
Here you adjust the mirror angle to alter the light path, the consequence is focus plain no longer 90 degree to your focus screen. Lets put in other way, if you have type S screen, only one horizontal line in the middle in focus will insync with your sensor, if your subject is upper or lower, either it will be front focused or back focused if you rely on your screen.
Again, I think you maybe fine in this case, just want make sure it doesn't alter your AF sensor path as I am not quite sure about that.
hope this helps.