it seems that we can ignore the site_node error, although I am still nervous about that. the fact that code is trying to select the root site_node before it exists doesn't sound right.
still haven't figured out why the ref-timezone package is getting installed at all, but you can work around it by installing acs-reference, then manually running ref-timezone-drop.sql manually (twice) and then installing ref-timezone.
I really don't like it. As Vinod observed, "everything seems to be ok"...