There is already a similar real-world situation with ssh keys.
Normally ssh keys are handled in a per user fashion and are stored in $HOME/.ssh/ on traditional multi-user linux distribution.
On linux distributions which encourage the use of ecryptfs for home directories.. the default ssh configuration which looks for ssh keys stored in $HOME/.ssh/ no longer works if the user is not already logged in via another means. Password login via ssh still works (if its enabled) because the pam stack for ssh is looking at the systemwide passwd/shadow information. If the user password was in the home directories, then ecryptfs-like encyption of home directories would have to be re-engineered.