Agreed - I was a virtualenv holdout until recently and even though it's a horrible solution with replication of junk everywhere it's the way to go.
Databases do it, Git does it, ZFS does it.
Ok the first two examples aren't filesystems but they can store files, so not totally irrelevant?
Relying on abstractions to simplify the architecture is a sign something might be right. Simply because simple things are less error-prone IMHO.
... oh, wait.