I have the same problem... Flying in the Patagonia..., or trying to do it, it's impossible!!!
I put my weather to Customize - Manually configured - Preset CAVOK. After DONE, Weather is Clear. Apply Changes. From the cabin I see the weather changes. Many clouds, etc... Back to Flight Configuration. Weather is Overcast... but I want it "Clear"... Do you now understand?
PS.- Using X-Plane 11.36r2 with macOS High Sierra 10.13.6 on an iMac 27 inch, 3,4 GHz Intel Core i7
PS2.- On the other side, the updated Cessna 172SP is great!!!
PS3.- It's not the X-Plane's update, but the Python scripts Noaa Weather!!!