GitConfigParser.set_value does not allow for setting multiple values for a given option.
One example of this is in the refspec documentation for git:
remote "origin"]
	url = https://github.com/schacon/simplegit-progit
	fetch = +refs/heads/master:refs/remotes/origin/master
	fetch = +refs/heads/experiment:refs/remotes/origin/experiment
If you try to call set_value twice with the two different refspecs above, only the last one will get set.. which makes sense since set_value seems to only support setting one value for a given option.