Of course it is obvious! But as always the must surely be more than one way to do it.
Products such as WEBMIN and CPanel are not meant for real sysadmins. They are meant for people who have to manage systems without being sysadmins. Some web hosting sites could have hundreds of boxes all with a standard install of, say, RH Linux, there is a standard complement of modules installed. But you may have 200 or more websites hosted on one machine and the people running the machine - possibly resellers, need to install modules with little or no knowledge of how to use CPAN - let alone how to admin the machine in detail. Running machines like this I have ofund only one ocassion when a module could not be installed through WHM/Cpanel. In that case I did it the 'real' way. But the other side of it is that such products as Cpanel give you a way of keeping all the mahor system components up to date, a way of installing a standard set of cgi scripts.
It may not be ideal, it is sure not pure but it is pragmatic. It works, it seems to be as secure as anything else. Of course there have been security exploits discovered. But darkorb (the developer) seem to be a lot faster than many other companies about advising their users and basically any updating that needs to be done, with the exception of a kernel upgrade, can be done from the GUI. Couple the system with very tight firewall screening and it works. In my case it saves me thousands of dollars per year, means all my hosting machines are using a common configuration and gives me an easy way to control them all.