We'd like to use this feature simply for our default course shell. In doing some testing, I created a new course, set the course menu the way we want it to be. I did not add any modules, pages or assignments.
I set the new course shell as a template, and added the course as the template in the administrator settings. Then I uploaded a flat file via SIS import with 3 courses: Test Course 1, 2 & 3. Test Course 1 did not have the template applied to it, but Test Courses 2 & 3 did.
I ran the test again, this time with Test Course 4, 5 & 6. Again, the first course (Test Course 4) did not, but Test Courses 5 & 6 did. Finally, I did a test with 9 more courses (Test Course 7-15). Again, the first course (Test Course 7) did not get the template applied, but the other 8 did.
So it appears that something in the algorithm is causing the first line in each upload to not get the template applied.