<p>Is it different from any other certificate I can generate via makecert or buy from some authority?</p>

It depends on what you are doing with it. If you want the certificate to be accepted by a browser in an SSL communication, then it must have a root certificate installed in the browser. The certificates generated by authorities already have their root certs installed in browsers.
If you are using the cert just to sign an assembly, then you don't need it. It depends on who is checking the cert and whether they care if the root is a known authority.
More here:
http://en.wikipedia.org/wiki/Root_certificate