I've just set up a Multi Configuration job: a master with no build responsibilities & 3 slaves (mac, win, linux). I see that the master clones a copy of the source repo into the root of one of the slave's workspace: workspace/projectname/contentsofrepo.
Then, the slave clones a separate copy of the same repo for its own purposes: workspace/projectname/label/osx/contentsofrepo.
I prefer to use the "Clean after checkout" option for my git projects, to ensure a clean workspace on a fresh build. However, with this enabled the master's git repo sees the slave's repo (again, located within the master's copy) as a directory not tracked by git and removes it, meaning that when the slave runs, it has to re-clone the entire repo, which takes about a half hour for our project.
I would expect the master & slave's copies of the repos to not overlap with one another such that they could be cleaned independently of one another.