Hey Michael, so I guess the question is, what do you want to be able to accomplish that you can't now?
The intent of Auto Echo is make it easy to rehearse and record different MIDI/Instrument tracks just by placing focus on them. Conveniently, the last chosen MIDI track will keep echoing when you move focus to the corresponding audio/synth track to adjust levels, or maybe tweak an FX while you trigger the synth from the keyboard and listen to the result. The case where you disable Input echo by using the echo button in the folder control is the only way you can get SONAR to temporarily show no MIDI track echoing, but when you move focus to another track, Auto Echo is re-invoked, and echoing of the last touched MIDI track is restored.
In my view this, this is all working as designed, and I don't see how any of it is a problem. If you want be able to have no track auto-echoing, just go to Preferences > MIDI > Playback and Recording, and disable Always Echo Current MIDI Track. And if you want to force some track to "Omni", choose All Inputs - Omni; it's the same thing by a different name.