The actual solution to the "missing mountains" was to reinstall:
This gets the original look of Zorin back, but it breaks SikuliX.
There does not appear to be a solution that lets you keep the original look and run an app like SikuliX which requires looking at the screen programatically.
Now that I know more about what's happening, I'd say a technical thread, maybe in GitHub is the best place to talk about why the "remember this decision" isn't working with SikuliX.