Focus mask to me is a post shot tool, i.e. on a Phase One back in the field it can be helpful to determine focus especially with a tech camera. I have never even thought of using it in post work in Capture One. I guess in a tethered environment it may come in handy. I tend to leave turned on on my Phase Back, but still rely on 100% to really determine true focus. I know Phase supports tethered attachment with Canon and Nikon besides their backs, don't think they have support for Fuji or the Lumix.
After reading your post I tried focus mask on my Fuji X-E1 files and it seems to work OK, having a bit of trouble in the sky.
In post work in Capture One, I always check focus with the 100% view.