I also observe this problem on virtualbox with debian as guest system. It does not depend if it is the pymol provided by deb system or compiled from source.
I've run the second command on the console and it worked (on the non patched pymol), however i couldn't test the first command as after the first command was run it always worked, even after restarting the console, restarting the computer and reinstalling pymol.
MacOS High Sierra with Python 2.7.14 installed via MacPorts
Pymol gives error on fetching from any https site when build with python 2.7.14