I have New Blogs Template and Multi Site Privacy.
I set the template to be 'don't index', but when I create a new site I have noticed that it is being set as allow search engines. Because I don't want sites to be indexed until they are ready to be domain mapped.
I'm fairly certain that this used to work, but recently it seems not, though I can't track it back to a specific release (of either) because I wasn't paying that much attention to it, I just have been noticing traffic from Google before sites are domain mapped, so have checked back to find this issue.
Does it work on your test system, or can you see the issue I can see?