Most comprehensive (corporate support based) panels have to take over much of the box. Its less of a support hassle and makes it easier on the admin, because it works out of the box. For instance, it probably installs its own Apache, email transport agent, FTPd, etc. IT would be a bit more of a hassle to support Apache 1.3.x, 2.x, Sendmail, Qmail, Exim, ProFTPd, vsFTPd, Wu-FTPd, FTPd, etc. and make it a lot more expensive.
They won't allow X to run. It uninstalls it and then keeps it from running. Just because it tries to make my security and application installation choices FOR me I wouldn't ever install it. Not that I would anyway.
http://cpanel.trustix.com/faqs/show1ca4.html