I am also experiencing this, also on 10.12.6. Like the others, I've tried fake-fullscreen, windowed, deferred rendering, and a number of the CMD-enabled tweaks, but nothing seems to help.
The issue is quite bizarre, it seems like some set of pixels in the ui elements are not recognized as being in front of the game world. When you hover over these pixels, no tooltips will popup (or rather, tooltips seem to be determined by the underlying world elements), and clicks fall through to the game world. There doesn't seem to be any pattern to which pixels are affected.
I have a feeling it's related to the resolution scaling on retina displays.
