One further thought. This is a change in behaviour (albeit to a script in Tools), so I'm inclined to say it's a new feature for 3.5, rather than a bugfix to be backported to 2.7 and 3.4.

For users of 2.7/3.4, the workaround is simply to rerun the script - it doesn't add directories it has already added, so it's safe to rerun to add newly created directories.