I think ignore_certificate_error should be defined inside the family file and has no effect in user-config.py.

As a workaround you can modify the ignore_certificate_error in pywikibot/family.py to make it return True. Then generate your family file using the generator script (hopefully there won't be any error now).

After that you can revert the change in family.py and define ignore_certificate_error in the newly generated file.