Yes, you are missing someting. :-) XEN_LOCK_DIR is used for a number of different things; but *only* "I am alive" init script files should live in /var/lock/subsys. (Presumably that's why it's a separate directory to begin with.) So the "proper" fix is to have the xendomains script check for the existence of $XEN_LOCK_DIR/subsys and use it if available. See my original patch submission for more details [1].
So, I've tested the packages and they work for me, let me know if you have any problems. :-)
Oh, good! Thanks for the explanation.
Updated to 4.6.1-9 testing, and things are looking good: in particular, I confirm domUs were saved+restored on dom0 restart.
Thanks again,