SystemRepository is a FileRepository and all FileRepository have \ThingworxStorage\repository as default parent directory. I din't find any option in the composer to configure this path for a particular FileRepository.
But you can create folder(s) in SystemRepository if it helps in your requirement.
You can create other repositories if you want, I don't know if it fits your requirements.
On the other case, we have a similar situation and we use subfolders ( automatically created ) for each thing of our customer, and each customer has it's own repository, we wrapped almost all services to access to Thing's Folder, and mostly you can control everything from a security viewpoint. I have a case opened with "GetFileListing" permissions which allows users to list all contents of a FileRepository, and if you block it's access then almost nothing works.