After digging a bit deeper I found out that that the default configuration of 
/etc/apt/apt.conf.d/50unattended-upgrades is exactly the same as I had in my 
experiment i.e.
- the ${distro_id}:${distro_codename}-security origin is ENABLED
- the ${distro_id}:${distro_codename}-updates and others origin are DISABLED

The consequences are the following. A fresh install of Ubuntu LTS e.g.
16.04 keeps installing the *-security updates, but not the *-updates
ones. The number of packages with new versions in *-updates repository
keeps growing unless somebody installs them manually. It is a couple of
clicks, but still many people never do it. As the list of upgradable
packages grows, unattended-upgrades get slower and slower to the point
that it may take hours to complete.  Effectively, the automatic updates
may no longer work at all depending on how a given system is used. Also
the user experience gets worse with CPU busy executing the unattended-
upgrades script.

All in all, I consider it a serious issue that requires attention.

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https://bugs.launchpad.net/bugs/1396787

Title:
  checking trust of archives eats a lot of cpu

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