Technically, the FTP protocol can do this as well, and so I have added support for it with the FTP protocol too. I verified this using the command line client "curl". Its still a bit of a pain dealing with all the certificates, so I'll be writing up some entries in my Wiki to help people with the process.
The summary? CrushFTP now supports FTPS client based certificates for authentication where the common name is the username. The cert the user provides must exist in your trust store file as a certificate that was issued from your server, or it won't be accepted.