systemd-update-done.service is a service that is invoked as part of the first boot after the vendor operating system resources in /usr have been updated. This is useful to implement offline updates of /usr which might require updates to /etc or /var on the following boot.
systemd-update-done.service updates the file modification time (mtime) of the stamp files /etc/.updated and /var/.updated to the modification time of the /usr directory, unless the stamp files are already newer.
Services that shall run after offline upgrades of /usr should order themselves before systemd-update-done.service, and use the ConditionNeedsUpdate= (see systemd.unit(5)) condition to make sure to run when /etc or /var are older than /usr according to the modification times of the files described above. This requires that updates to /usr are always followed by an update of the modification time of /usr, for example by invoking touch(1) on it.