With the RoboHelp files, do you mean the *.fpj files, the *.apj files etc? Without these files, you don't have a RoboHelp project. Additionally, RoboHelp also stores content in the project files (Table of Contents, Index, Language resources, etc.)
RoboHelp gives you an all or nothing scenario. You can put all files in GIT manually, but you can also use a GIT to MSSCCI plugin to handle it from RoboHelp. In which case all files are added to source control. If you want different behaviour, you will have to try to set it up yourself. RoboHelp doesn't support it.