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The two modes are either to store the syskey protected boot locally or on a floppy disk. In other words, the user would always require the floppy disk to logon.
So indirectly you could say it was protecting EFS files – because an attacker would require the floppy disk to boot up with before they could even log on but actually it is protecting the authentication procedure.
In Summary
To truly have an effective EFS infrastructure, you should use Windows XP clients with Windows 2003 servers and wherever possible some kind of layered defence model.
I.e. in this case – if possible physical security, authentication security, file system security, encryption security.
Finally it is important to teach your users the best practices outlined here. and be sure to read http://www.microsoft.com/technet/security/topics/cryptographyetc/efs.mspx for a larger overview.
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