I have narrowed down. This bug was introduced by the fix in #1618900.
That tries to fix the problem of the the unattended-upgrades.service
by letting it depend on network.target and local-fs.target.
However, that doesn't change any of the dependencies, it only makes
the race window larger.
After some experiments, the correct dependencies in the unit file appear
Which make it behave just like the SysV init script.
This change together with the patch I attached to this bug report
together should fix the issue and also fix #1618900 .
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unattended-upgrade-shutdown hangs when /var is a separate filesystem
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