This doesn't seem to be an issue if '%current-system' is parameterized,
as in the following.

#+BEGIN_SRC scheme
(parameterize ((%current-system "i686-linux"))
  (with-store store
    (run-with-store store
      (display-exp #~(primitive-load #$(switch-system-program %system))))))
#+END_SRC

Regards,
Jakob