As far as I know, you 'can' configure SQL Server to use raw disk partitions (see Using Raw Partition in SQL Server Books Online). I don't know how far this goes, as I have never had to configure a system this way.

In the case of WinFS, I think the DataBase will not hold the files per se, just metadata to perform searching and cataloging. The files reside on NTFS partitions.

Cheers

Alejandro