From an end user's perspective Tarsnap certainly deals with files and folders. It outsources most of that work to libarchive, which is kind of my point.
The article says to "Encrypt things at the highest layer you can.", but you could imagine a backup utility doing encryption at a higher layer than Tarsnap does, with all the complications that would bring. And would it be even better if instead of file system level encryption, every application encrypted it's own files? I don't think so.
So maybe it should just say "Encrypt things at the highest layer that makes sense", which is kind of vacuous.
IMO it would make just as much sense to say "Encrypt things at the level where it's easiest to do.", where block level encryption is a strong contender. It doesn't give you every property you might want, but it's easy to get right.
