Turns out that the /etc/network/interfaces stuff I mentioned before was
a red herring, here is the actual problem.

Without overlayroot the (nfs) root filesystem is mounted at /, and on
reboot/shutdown /etc/init.d/umountnfs.sh will skip that mount point when
unmounting the network file systems (because of lines 49 & 50 of
/etc/init.d/umountnfs.sh).

With overlayroot enabled, the "root" filesystem is mounted at /, but the
nfs mount that is "under" the overlay is mounted at /media/root-ro,
which is NOT skipped during reboot/shutdown.

The fix I have in place is to change line 49 of /etc/init.d/umountnfs.sh
from:

    /|/proc|/dev|/dev/pts|/dev/shm|/proc/*|/sys|/run|/run/*)

to:

    /|/proc|/dev|/dev/pts|/dev/shm|/proc/*|/sys|/run|/run/*|/media/root-
ro)

And I am able to reboot/shutdown properly.

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https://bugs.launchpad.net/bugs/1165886

Title:
  overlayroot prevents shutdown / reboot under nfsroot

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