Because it’s confusing to use the term this way. In programming “purely functional” means no side effects; writing files to disk and mutating the state of the host system is a strong set of side effects.
Of course, you probably want some side-effects, so you'll put symlinks to the stuff you want in your user profile, or into a .envrc file in the root of a project.
Paired with use-package it makes emacs configs very compact, typically you can have a single conf file + the versions file for everything related to ones setup. That makes it very easy to transport.
Even if you use nix/guix it's more convenient imho to use straight.el for emacs, as it's standalone as long as emacs is available.