How annoying. The camera can be set up to show blinkies on the screen, but it really defeats the purpose of an EVF, in that you should be able to get the correct exposure just using the viewfinder and rarely "chimp".
I haven't had an issue with the histograms not matching, I'd have to get the camera out to play with the settings to see if I could reproduce the effect you describe.
I've thrown out the whole ETTR with the X-T2. I still have the histogram showing in the viewfinder, but I look for detail in the highlights and judge my exposure based on what I see there. Shadow recovery works just fine in post on the whole.
Just off the top of my head, you could try changing the metering mode and play with the picture effect off/on.
David