Hm, didn't think about that. Makes sense though.

In case anyone else runs into this, my workaround is to delete
/etc/pam.d/common-* before running pam-auth-update. Still requires
special handling in the install scripts, but at least the config is in
debconf where it belongs.

-- 
pam-auth-update ignores debconf settings
https://bugs.launchpad.net/bugs/682662
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