I am quite confused.
I use Battery 3 with Sonar, and have a custom kit I created in Battery 3, where each drum cell gets assigned to its own outputs, and then I simply created a bunch of tracks in Sonar and assigned each track to one of the outputs.
And separately, I frequently load multiple instruments into Kontakt 5, making multiple output assignments, and also have no trouble with Sonar having separate tracks pointing to the various outputs from the multiple instrument outputs coming from Kontakt 5.
From the above, it would appear that Sonar doesn't have any issues with assigning the tracks, and it would seem that for instruments that Kontakt also does not have issue with presenting multiple outputs to Sonar, so it would seem that closer examination of exactly what you are doing within Kontakt would be of value.
I will play around with what you are trying to do and post back later today on what I can figure out. I have to leave early this morning for a doctor's appointment, and will be back here in the early afternoon, so I hope to have some additional information for you by late afternoon or early evening today.
Bob Bone