[dnanian]

Smart Update should work fine with your restoration: the blog post that discusses this issue was during the beta of El Capitan. Apple fixed the issue, and restorations work as expected.

That said, you should not copy El Capitan from Snow Leopard. That's not going to work. You need to use El Capitan or later. This is generally true: you shouldn't copy later versions from earlier versions: the OS's file system changes, and only the newer OS versions know how to deal with it properly.

As such, you'll want to migrate from the copy during first boot of the new install.