Correction! apt-get update is obedient when synaptic is not. apt-get install *nvidia* is showing the error line once. Synaptic shows the error line when invoked, and when ok is pressed, it exits. Tasksel, when invoked, shows the error line numerous times and exits. The error lines, as stated earlier, are displayed despite the 2nd line in /etc/apt/apt.conf.d/00knoppix has been silenced.
So apt must be accessing another configuration file from somewhere.
The maintainers of Apt appear to be oblivious of the fact that while apt.conf is nowhere to be found, apt still has the file mentioned in its list of files.