This is by design. The RunOnce page was not removed from the installation. Instead, the page has been changed to not allow anyone to run it. What happens is if the DefaultPortalID appSetting in the web.config file is not '{0}' then the RunOnce page will now just redirect to the default.aspx page. The only time that the RunOnce page is run is if the DefaultPortalId setting is '{0}', which happens on installs, but not on upgrades.
I have placed the installer back online.
Jeff