There are differences in how you'd use them. Scheme is very focused on a minimal core and extension through macros and similar constructs, whereas, as far as I

There are differences in how you'd use them. Scheme is very focused on a minimal core and extension through macros and similar constructs, whereas, as far as I know (nb: I don't use emacs) Elisp has a lot of pre-built constructs that are used far more. Also, Guile being the implementation chosen is not incidental, the GNU project is moving towards Guile as an extension language everywhere (The big example here would be GuixSD).