Hi Mark,
The latter is similar to etp. Basically each etp instance is a package instance, so it has site node. It also creates a cr folder.
The former I think is how aD cms does it. CR folders is out of synch.
I think this is a good topic to discuss in the IRC meeting. Which way to go.
The advantage of synch site node and cr folder is that the CMS will act more like a site. The disadvantage is that its less flexible. So if the cms is less site centric, say displays items on a category basis. Or maybe content is displayed in more than 1 way. So in sync fits more for simpler cms, while out of sync fits more in bigger cms.