The video is using Logic. The side chain in the video is part of the Logic's routing not a feature in Stutter Edit. The routing used in the video is not necessary in SONAR. Unlike Logic, SONAR can apply Stutter Edit directly to an instrument track.
Still not clear on what the issue is. MIDI note on, Stutter Edit plays the gesture bound to the note, no MIDI note data or MIDI note off and the Stutter Edit effect is off and unaffected track plays through. Only when the Dry Gain is on does Stutter Edit mix in the dry signal when the effect is playing. This is the case with the video too once the Stutter Edit bus output is turned off.