Hello,
as far as I can see, no user called "System" ever existed in any of my Repositories - no matter the Alfresco version (currently checked a 4.2.4). I must admit, I have never used the "runAs" configuration on AlfrescoScriptTask - whenever I want to execute something as the System user, I use a Java delegate and do a proper AuthenticationUtil.runAsSystem().
So far, I can see no change concerning the "System" user behaviour in Alfresco 5.0
Regards
Axel