It moves around as well. There's a huge distinction between Linux _as a kernel_ and "Linux" _as an operating system_. The kernel has the same layout across all the distributions / operating systems, but everything else is up to the particular stack that distro chose. Gentoo is different from Redhat which is different from Debian, etc.

You can do what you describe without changing the kernel, but you would need to modify the userspace environment. One of my toy projects has been trying to run all "user" applications in filesystem sandboxes because I'm sick of how many random "dot-files/directories" get created in my home folder.