There used to be similar UI layout issues prior to SU2 (buttons halfway visible and co), but SU2 makes it far worse and plain unusable (whole list of possible atc answers is invisible most of the time).
It is to a point where i am currently writing a small package with a custom simplified ATC UI so i dont have to constantly switch in/out of VR.
Also in non vr mode, we still have weird layout issues with halfway visible buttons. Nothing like in VR but still pretty annoying.