I have the same problem but I just worked around it for a year. I think when I added extensions I did it from a dock, and when I want to use the menu to open a new tab, you may see, it is flashing, but then if you open the menu with the keyboard minimized, it is not flashing.
My understanding is that the user @Emma did some kind of great upgrade for this, but because I was extremely lazy and did not search up how to install the customization, it was always missing on my device. I think the improvements/customizations are included on Crimson by default, and notably when I recently installed Crimson it had absolutely none of these problems.
But it had other stuff totally broken, such as the device camera not working, so reinstalling to Crimson is not a solution for now. That probably means most users who care more than I do about it are using the Firefox configurational fixes from Emma.
Edit:
Possibly relevant link: Mobile-Friendly Firefox Customizations for Librem 5
Possibly irrelevant link: Enough is enough with Firefox - #2 by amarok , ( or enter about:mozilla in your Firefox URL bar)