Just a thought which has occured while helping a client out with an install of some software:
We uploaded a tar.gz file, unzip’d it and configured the software for them, all as our ‘super user’ to do through command line, however we then have to set the permissions back.
A feature which could be looked at being added, would be a big button in SiteWorx (or possibly Nodeworx) which read “Reset File Ownerships & Permissions” which put all the files in their home/html directory back to their ownership.
Just a thought…