Comment 3 for bug 246381

The APT cron job has a random delay to avoid having many thousands of machines hitting mirrors at the very same time.

Perhaps we should rename it zzz-apt as to not delay the other jobs randomly? or we could use /etc/cron.d instead of cron.daily.

As a workaround, you can move /etc/cron.daily/apt to /etc/apt-daily-cron and add an entry in /etc/crontab such as:
25 6 * * root /etc/apt-daily-cron