Also facing this issue, it's weird that newer pam-auth-update also ignores 
default option in pam configs. So now it's not possible to non-interactively 
enable new profile (but it was working in trusty).
Here's updated script to add one profile (mkhomedir) to current set of profiles:

#!/bin/sh

PROFILES=$(debconf-get-selections | grep libpam-runtime/profiles | cut -d ' ' 
-f 2- | sed s/\,\ mkhomedir//g)
PROFILES="${PROFILES}, mkhomedir"

for profile in /usr/share/pam-configs/*; do
        profile_name=$(grep Name: $profile | cut -d ' ' -f 2-)
        PROFILES=$(echo $PROFILES | sed s,$(basename 
$profile),"${profile_name}",g)
done

cat > $1 <<EOF
libpam-runtime/profiles="${PROFILES}"
EOF

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https://bugs.launchpad.net/bugs/682662

Title:
  pam-auth-update ignores debconf settings

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