As I have mentioned in prior post. I have been building for years. We built a system called publishtown which is basically the same thing as a wp multisite but cleaner in many ways. I understand the cross compatibility issues that wp plugins run up against but there has to be a better way to build a replicating template website builder.
Here is how I managed it prior. I had folders for the web templates. Then inside this folder I had a user folder similiar to the blogs.dir concept. So I would then use the include path logic built in php and simply check the user folder for the file then the main template folder. This way I could manage the website from the main folder.
In wp since all the data is shoved into the wp_post table it would have to be a database pull unless you built a system that ran off cache files but that is probably not going to happen. So with the database pull from the post table, it could be as simple as this a query join across the site post table and the template post table where page or page_id = ORDER ASC then just pull back the top row. This simply says if this page has been replaced by the site then pull the site page if not then pull the template page.
Now I know the problems with menus and copying data, etc... So here is how I see it working, this will only work if your site menu is not built off the post table. It has to be built through the menu builder. Then you simply do not copy over the post table.
Obviously I lack some understanding here because I have not been using wp that long but the current way of handling replicating websites is a pain. I have thought about running everything through custom page templates and doing it myself and probably will for the short term but I believe that there has to be a better solution than the one currently being developed.