Creating a hole using /fill command and replacing the roof to solid blocks should make the hole completely dark but it sometimes unsync the Client Light with Server Light as client light says there is light from sky while there is no sky access and no way for light to get in. Server light is on 0 light but because of client light it still shows the area bright.

I saw the opposite of it happening. The place had direct sky access but was completely dark and placing light sources and breaking them does not fix the darkness.

It is not a big/ game breaking issue but it still is annoying to fix it by hand, making /fill command a bit harder to use (for me).