I have posted my question on stackoverflow.com ( http://bit.ly/9UeChD ) and wordpress.com ( http://bit.ly/aTSo21 ), but still no joy.
Hoping someone on HN has what it takes to rewrite "http://site.com/app/alpha/beta" to "http://site.com/app/?a=alpha&b=beta" and then let the Wordpress rules route it through index.php to the "app" page, which can pull the parameters from $_GET.