Sub-sites within Sub-sites within sub-sites within a network (sub-sub-sub-sites?

I’m working on a wp server at a university, and exploring how to host a lot of sites while we maintain the structural hierarchy that we have standardized on for other web services*, and I’m running into a problem.

Our server is setup to host sites following the format:

https://wp.school.edu/{username}

For a pilot project with the art school, we want to set up eportfolio sites under the url:

https://wp.school.edu/artSchool/designDept/eportfolios/{username}

In theory, I would prefer if

https://wp.school.edu/artSchool/designDept/eportfolios      was a subnet of
https://wp.school.edu/artSchool/designDept/                       which was a subnet of
https://wp.school.edu/artSchool/                                          a subnet of
https://wp.school.edu/

And that any of those subnets could have sites within them.

So here’s where I am:

1. I installed WP Multi-Network,
2. I was able to get the https://wp.school.edu/artSchool/ subnet path working without a problem, BUT
3. while I can make a network with the path https://wp.school.edu/artSchool/designDept I get 404 errors when I try to access the admin area of designDept
4. and although the default content of the site loads, the theme files 404 as well.
   ( anything under
   https://wp.school.edu/artSchool/designDept/wp-content/themes/twenty-ten)

Is this a limitation of the plugin and/or wordpress? Or is it possible that it can be done, just that I’l need to write a more complicated htaccess file?

* it may seem a bit old school (ha ha) to want to retain the hierarchy, but many of the use cases are things like an instructors information page, or student assignments, etc. We partially want to use multinetworks as a way to manage templates & settings for different schools & departments, and partially as a structural organizer (we have like 15 colleges and hundreds of departments, all of which have different programs, many with similar names – for example there are several different colleges with a department that is referred to as “communications” but is actually called communication therapy or science or blah blah blah – you get what I’m saying, I’m sure)