Reg Developer has recently published an article exploring the "support vacuum" created when a distribution substantially modifies an application's default configuration in its package system. From the article:
They've configured it right, but Apache ignores it because it needs some extra distro-defined magic to activate the configuration file in question. Now they're banging their head in desperation, and we can't help because we don't know the magic. And we get the blame.
The author uses Apache and Debian/Ubuntu as an example, but this is an issue with most (if not all) distributions. I've had similar problems myself trying to get Apache configured correctly under Gentoo (though the situation has improved substantially in recent versions).
Obviously a distribution will have to make certain modifications to a given application to make it fit in properly with the rest of the system. Sometimes there's just no avoiding it. But the author raises a great point; who will support the applications? If the application developers don't know what changes the distribution made to the application, and package maintainers do not know enough about the application to answer a question, who does it go to?
I hope package maintainers read this article and take it to heart. As I stated above, there will likely always be changes that need to be made here and there to provide a consistent feel across the distribution, but it's important to remember that the more drastically the application is changed, the more difficult it will be for the distribution's own users to get help.
Article link:
http://www.regdeveloper.co.uk/2006/11/04/apache_packages_support_vacuum/