What I did on my account was install awstats in my account directory, and have the buildstaticpages script put the output in a directory in the user's web directory which is password protected. All my cron scripts run under my main account. This works well unless the user wants to be able to update their stats whenever they want.
With a custom PHP install you'd have to copy the php executable and the ini file into each users cgi-bin directory, and change their .htaccess file.
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