I disagree for these reasons:

1. This decreases composability. With encrypted filesystems, I can't mix and match filesystems and cryptosystems to suit my needs. There is no reason they need to be convolved.

2. This increases complexity. Now, the person writing the software has to be an expert in both filesystems and cryptosystems if they want to do a good job. There is more room for error. (You might say it violates the UNIX philosophy of "do one thing and do it well".)

3. This leaks information to an attacker. They know the layout of my files even without my password. I'm more comfortable with absolutely everything looking like a giant monolithic block of random data.