If the Course default setting of Visibility is set to "This course is available to students" then despite the IMS Enterprise plugin specifying "Create new (hidden) courses if not found in Moodle", the course will be visible.

This is because Moodle will not apply the default course settings, and is no longer set to make a course invisible by default. This probably just needs the wording changed to "Create new course if not found in Moodle" and perhaps a note outlining that default setting will be applied, and maybe a link to the default course setting to alert people to this fact?