I use TB 3.0 and am storing my several e-mail profiles in folders other than the main profile's sub-directory. MozBackup cleanly backs up my profile meta data, but not the actual message stores. There is no error message, no notification whatsoever, just a success message at the end of the backup. If I would have trusted in it and not double-checked because I found the backup's size strangely small, I might have gotten into problems in case of a restore. So I am doing backup/restore manually again, like before.
This can be considered a bug. I suggest to fix it or extend the functionality, respecively.