Hi, yes, when used in a server, RStudio limits file write access to the user's "home" folder. The user should be able to see system level files, but not the files in the other user's "home" folder. You would have to setup new Linux users for each person that needs access.
If you want the access to be controlled by AD, then you are probably going to need to use the commercial version of RStudio, called Workbench (RStudio Workbench - RStudio). That version provides integration with several different authentication systems, including AD.