>> You mean to do away with the KEEP-WINDOWS argument and keep windows iff
 >> `window-state-put-keep-window-functions' is non-nil?
 >
 > Yes, I meant removing the KEEP-WINDOWS argument.

Patch attached.  I now provide only one hook I called
'window-kept-windows-functions' which is run by both
'set-window-configuration' and 'window-state-put'.
Tested with

(defun foo (frame windows)
   (while windows
     (let* ((quad (car windows))
	   (window (car quad))
	   (name (buffer-file-name (nth 1 quad)))
	   (buffer
	    (and name (find-file-noselect name))))
       (when buffer
	(set-window-buffer window buffer)
	(set-window-point window (nth 3 quad))
	(set-window-start window (nth 2 quad) t)))
     (setq windows (cdr windows))))

(add-hook 'window-kept-windows-functions 'foo)

(let ((window (selected-window))
       (buffer (pop-to-buffer
	       (find-file-noselect "...")))
       (window-1 (split-window))
       (window-2 (split-window nil nil t))
       configuration)
   (set-window-point window-1 5000)
   (set-window-point window-2 10000)
   (setq configuration (current-window-configuration))
   (y-or-n-p "Configuration saved ...")
   (delete-other-windows window)
   (kill-buffer buffer)
   (y-or-n-p "Configuration reset ...")
   (set-window-configuration configuration)
   (message "Configuration restored"))

(let ((window (selected-window))
       (buffer (pop-to-buffer
	       (find-file-noselect "...")))
       (window-1 (split-window))
       (window-2 (split-window nil nil t))
       state)
   (set-window-point window-1 5000)
   (set-window-point window-2 10000)
   (setq state (window-state-get))
   (y-or-n-p "State saved ...")
   (delete-other-windows window)
   (kill-buffer buffer)
   (y-or-n-p "State reset ...")
   (window-state-put state)
   (message "State restored"))

 >> This would be up to you to decide.  Only some practice can tell what's
 >> better here.
 >
 > Otherwise users won't be able to use this hook for existing commands
 > that don't set the KEEP-WINDOWS argument.

OK.  But note that we now run this hook even if nothing in the window
configuration changes, typically, when calling 'read-minibuffer'.  So
use it with due care (for example, have the tab code bind it exclusively
around its calls of 'set-window-configuration').

martin