Unattended upgrades in Debian will not upgrade packages from third-party repositories (for example dotdeb.org) by default. It can be easily enabled editing /etc/apt/apt.conf.d/50unattended-upgrades.
/etc/apt/apt.conf.d/50unattended-upgrades
Unattended-Upgrade::Allowed-Origins {
"${distro_id} stable";
"${distro_id} ${distro_codename}-security";
"${distro_id} ${distro_codename}-updates";
"packages.dotdeb.org stable";
// "${distro_id} ${distro_codename}-proposed-updates";
};
See this page how to enable other repositories.