Multisite: Install parent/child themes in sub-directory?

Let me eloborate...

I have Multisite with some clients have more than one site.

Rather than the sites being used at Administrator level by Muggles, it's by agencies who use my platform.

Now...re: themes...

As we all know, themes are installed in /wp-content/themes

Is is possible, easily, for each agency (e.g. agencyone, agencytwo, etc) to be installed at the machine level at...

/wp-content/themes/agencyone
/wp-content/themes/agencytwo

etc...

I use a file manager which can set permissions, etc and the directory structure thing is the only area I have a blind spot on...