A specious argument. You are right that open-source OSes like Linux and FreeBSD allow users to inspect their source code, to read and modify their system at the kernel level. This is also utterly useless to the 99.99%+ of computer users who don't even know or care to program, let alone muck around with a messy million-line codebase of C.
Writing kernel code isn't the only way to configure Linux. For example. the /proc file system lets users configure many aspects of the kernel without even rebooting.
Also, a lot of the userspace configuration is much more accessible to users and scripts through /etc than through the registry editor. I admit that I don't have a lot of experiance installing XP so correct me if I'm wrong, but linux gives the user a many ways to configure the installation that arn't available in the XP installation.