However the secondary program that does the copying/installing of the patch once it's downloaded will require user permission each time a patch is downloaded.

In general true for sane setups, but as a note: this is only true if the game is installed in a secured central location. A number of games don't have a real installer, but rather just a small launcher that you run directly which installs the game into %HOME% or %APPDATA% or the like (optionally in some cases).