I work in backup (this has become a core part of my business: http://macdaddy.io/mac-backup-software/) and part of the reason I wrote that is because of the continual reports of Time Machine backups failing to restore when people needed them. The numbers are huge. I wouldn't touch Time Machine in any conditions. I would manually backup before using that. This may be anecdotal evidence, but if you want to see some of the issues people run into with Time Machine just read through some of the posts people make about it: https://www.google.com/search?q=time+machine+backup+failure&...
Most of this is indeed directly related to directory backups. I also do Snapshots of sorts, but it only makes hardlinks to files, not directories. That proves to be remarkably more reliable.