Ubuntu *has* to assume those directories exist (as noted above).
It appears that you failed to set up your very custom installation
correctly, you would have needed to make /var/run and /var/lock
underneath /var. The installers all take care of this, and it's noted
in the Wiki under custom installations.
** Changed in: initscripts (Ubuntu)
Status: Confirmed => Rejected
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missing /var/run in root partition fails many services
https://launchpad.net/bugs/51452
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