Will OSX Lion support filevault encryption on bootcamp partitions?
Personally I think it is unlikely, as Windows would need some way to decyrpt the drive, or the operating system would need to unlock the drive before Windows itself booted.

There are some screenshots of the process, and it looks like when they said whole disk they meant not just user home folders, but applications and root folders as well.

http://www.appleinsider.com/articles/11/02/28/inside_mac_os_x_10_7_lion_file_vault_full_disk_encryption_and_cloud_key_storage.html