Hello
I also encountered this recently.
After checking source code of emacs and guix, I think this is because emacs is built without dependency: libxrender.
So I customized the relevant packages for test, as follows:
```
(define-public emacs-4me
(package
(inherit emacs)
(name "emacs-4me")
(inputs (modify-inputs (package-inputs emacs)
(prepend
libxrender
libxt)))))
(define-public emacs-exwm-4me
(package
(inherit emacs-exwm)
(name "emacs-exwm-4me")
(arguments
(substitute-keyword-arguments (package-arguments emacs-exwm)
((#:emacs _) emacs-4me)))))
```
Background transparency works for me now.