The exposure compensation thing too is a bummer as I really need something like the XF16-80mm f/4.0 OIS or even for my XF18-55mm f/2.8-4.0 OIS to just work so I can reframe during shoots. You can't really shoot documentaries nearly as effectively with just using zooms as variable primes. I roll constantly and have captured some magical things when I was rolling and moved the zoom to reframe. The exposure compensation has ruined some many great shots.
This thread suggests that enabling Auto ISO helps with the flicker issue when zooming with Fuji lenses:
https://www.fujix-forum.com/threads/xt3-18-55-lens-light-flicker.89114
This isn't really a full solution of course, since depending on what you are shooting, Auto ISO could be problematic for other reasons. But it still might be worth a try to see if it makes a difference.