I’m not sure, as I wasn’t part of the implementation team that did this work. Maybe contact your Squiz account manager to try and get some help from them to try and get the background and context around this particular implementation?
But like others have said on this thread, having two separate site assets like that is often done to separate content and design. It makes it easier to do things like applying workflow, permissions, designs, etc from a single root node.
As bkelly said, you can use the XML import tool. A few step-by-step instructions here: https://matrix.squiz.net/resources/templates#import-instructions
In regards to providing some more contextual documentation around that site structure, it is something we want to do, but we are actually planning on releasing an updated version of that “site boilerplate” as part of the upcoming 5.5 release, one that is mainly structured the same, but with less default assets in the import. Once we do that we’ll aim to have some additional documentation to follow.
Again, it’s just a recommendation, not a requirement to get the best of out the software. If there are other site structures people have used with great success, we’d love to hear from you so that we can keep improving this template.
Hope that helps.