I think it doesn't make sense for a user to have more then one dotFOLIO. To me that goes against the point of the package.
Thus is a user is likely to be a member of more then one group dotFOLIO should be mounted at the top level. Example a traditional university where studnets take multiple courses.
However, If you are running a site where you are creating dotFOLIOS for a use case like multiple schools, where an advisor might be a member of more then one group(school) but you expect it to be very rare that a student is, then I think multiple dotFOLIO mounts might make sense.