It means when you create a new course, should the repository type Legacy files be present in the new course? The default for Moodle 2 is no. This setting is essentially a course default setting.
The Legacy files repository is only present by default in courses upgraded from from Moodle 1.9, since they all had a Course files area which is translated into the Legacy files repository after the upgrade to 2. You could manually add Legacy files to any Moodle 2 course if you want, provided it has been enabled in Site admin > Plugins > Repositories - but don't.
Since you are restoring a course, Restore will abide by what was in the original course settings and content.
So, either your 2.4 course had a Legacy files repository in it and Restore did the proper thing, or your 2.4 course did not have Legacy files and Restore made a mistake and you've found a bug.