Hi Jakub Sisak. I realize this is an old post, but I ran across it so wanted to see if this behavior in ArcGIS Pro is still affecting your work.
From what I can tell, the flashing doesn't actually prevent me from continuing to work, but if this is still an issue you're seeing, you could submit it as an idea on ArcGIS Ideas. So far, I haven't heard this mentioned by anybody else, but it would be good to get a gauge across the broader community. Thank you!