A really simple way to fit platform- or machine- specific customizations into the customization interface is to use themes. Just put this in your .emacs:
;; Load up any customization themes based on the system-type and the
;; system-name. This allows us to use the customize interface (via
;; customize-create-theme) to set up platform- and system- dependent
;; customizations. To create a set of customizations that applies
;; when (eq system-type 'darwin), just create a theme called
;; "system-type-darwin". See
;; [[info:emacs:Custom%20Themes][info:emacs:Custom Themes]] for more on
;; themes.
(dolist (x '(type name))
(let* ((var-name (concat "system-" (symbol-name x)))
(var-value (eval (intern var-name)))
(theme (intern (concat var-name "-" (format "%s" var-value)))))
(ignore-errors (load-theme theme))))