Originally reported by Denis Otkidach (Bitbucket: ods, GitHub: ods)
Arguments show_missing and skip_covered of Coverage.report() have non-None default values that causes parameters with the same name from config overwritten unless you explicitly pass Nones to Coverage.report(). That is the reason why pytest-cov plugin doesn't allow setting these parameters through config file.
Changing default values of show_missing and skip_covered of Coverage.report() method to None solves the problem.