The preference you speak of, wasn't present in any recent (I checked back to Lion).
After looking through the updates to Mail in Mavericks, it looks like I have bad news.
We'll look at the exact implementation details in a later blog post.
If you can't wait until then, feel free to browse the official document on the topic.
One possible way to set up the second option (i.e., routinely moving messages out of your inbox) might work well for you.