I had these occasional screen flashes with Nova when switching back from an app to the Nova launcher (not sure why, somehow some weird interaction with gestures). I suspected it had something to do with the Pixel launcher, so disabled Pixel launcher.
Then indeed, the screen flashes were gone.
However, the "recent apps" list (swipe up and hold) does no longer work then as the recent screen (
https://developer.android.com/guide/components/activities/recents) is implemeted by the Pixel launcher.
So I was in a dilemma:
a) eliminate screen flashes -> disable Pixel launcher -> no more recent apps screen
b) leave screen flashes -> leave Pixel launcher enabled -> recent apps list
So now, as said in previous post I have:
Nova + Pixel launcher enabled + 3 button navigation (no gestures) + hide nav bar + FNG (fluid navigation gesture)
That solves the problem of the screen flashes for me (and has additional benefit of more configurable gestures).
In addition, the other issue which I had was: if you go back from an app to Nova launcher and very quickly tap an icon on the Nova screen then sometimes that tap would not be picked up (waiting 0.5sec before tapping would solve that problem). Again, I suspect some weird interaction between Nova and Pixel launcher. But with the above combination also that issue seems to be gone for me now. So I'm much happier.