There is no reason you need to use webwork2 itself as the front page.
You can have two standard html pages
https://ucschool.edu/school1
https://ucshool.edu/school 2
Each of these would have standard html links for the courses at the separate school of the form:
<a href="https://ucschool.edu/webwork2/school1course1"> Course1 </a>
Each of the two front pages would point only to courses for that school.
The link above would be on the school1 page.
You have to maintain two additional html pages but that is less trouble than trying to run two versions of apache. :-)