GitConfigParser.set_value does not allow for setting multiple values for a given option.
One example of this is inthe refspec documentation for git:

remote "origin"]url = https://github.com/schacon/simplegit-progitfetch = +refs/heads/master:refs/remotes/origin/masterfetch = +refs/heads/experiment:refs/remotes/origin/experiment

If you try to callset_value twice with the two different refspecs above, only the last one will get set.. which makes sense sinceset_value seems to only support setting one value for a given option.