For the structure @chris.prener lays out, you'd have to have one project with its home directory at the top most level. That would then control the version control. Then that project could see changes below it and manage the repo. That's really not ideal, I think. The lower level projects would not be able to manage the git repo and the upper level could not open the lower level projects without borking paths... So, yeah you can do it, but it's not ideal.
Slamming all their junk into one repo is a bad design decision. But you kinda already get that, I think. To work within that confounded structure I think taking Chris' cue and using git desktop makes total sense. And just avoid the rstudio git integration when you work with that client.