The difference depends on the distro. I use Gentoo and have used it for years and have not messed with other distros to much, other than installing Kubuntu for my brother.
As for config files, that is usually handled by the package manager. The package manager is what actually installs files so the package manager does this by where the people developing the distro thinks it should go. Once installed, there is sometimes a tool to config things or sometimes, it is done by hand.
With Gentoo, we have a file called a ebuild. That file tells the package manager what packages it depends on. It also tells where files go during the install. It also can set USE flags which changes how a program works or what a program supports. Gentoo is a source based distro so it depends on the admin to set all this up before hand. There is another set of files that the user can use to tweak these settings globally or even just for one package.
A distro like Redhat doesn't give that sort of control. When you install a package in Redhat, the people at Redhat have done most all that for you. Basically, they enable most everything whether you need it or not, which is why some people use Gentoo. At any rate. Redhat is a binary based system. Basically, it is faster to install but you have less control of options.
You are right about the kernel. Most all distros use the same kernel although some patch kernels in certain ways to either enable things, disable things or just add features that the distro needs.
I don't generally get into the details of other distros. I been using Gentoo for a long time but have used Mandrake way back. I have installed Kubuntu and update it but not expert enough to tell you why they set things up the way they do. I have found that every distro has something weird about it. It never fails.