If you hit the Edit configurations... button in the submenu appearing when clicking on your currently selected run configuration in the top right of PyCharm, you are able to edit the fields (and therefore also the working directory) of Python run configurations by selecting Python from the Templates (also called Defaults in versions pre-2018) and specifying the desired values.
Don’t forget to hit Apply/OK before creating new run configurations, which should now contain the default values you specified!
As far as I know, these defaults are local to one project.
See also: https://www.jetbrains.com/help/pycharm/2016.2/creating-and-editing-run-debug-configurations.html