Excluding Overwatch.exe doesn't seem to resolve the issue. I tested it on the training map and it's far less noticeable, but still there. Framerates were pretty much the same with WindowFX on or off, but when moving and tracking with it off it was much smoother and easier to target focus. Maybe it's FreeSync related? This decline in severity is likely because yesterday first map I played was in a competitive match on King's Row.
I tested lastest DOOM (max settings) and didn't get notice the issue. Maybe due to motion blur?
Both were in fullscreen exclusive mode. Maybe it's something about Overwatch's game engine? Maybe it's something about FreeSync or AMD driver?
In any case, a means of disabling WindowFX on exclusive/borderless fullscreen detection, or game detection/blacklist would be great!
Sans that, right clicking system tray icon for menu item to tick Enable (or alt+click or something) and tray icon indicating disabled mode would be cool, too.
I love the features of WindowFX and while having it handle everything would be great, a little user intervention isn't much to ask for when it comes to games that might not play nice with it for whatever reason.