I have been a long-time NI user and have Kontakt 5 currently running -x64.
I use multiple instruments in Kontakt all the time, but I reset all of the output channels using that batch function to clear the output section and recreate channels with 1 stereo channel for each loaded instrument.
I then rename them to match easy to read output channel names, like PIano, Bass, Organ, etc. That makes for easier reading at a glance for me back in the assignments in the console.
Also, when I insert Kontakt 5 into the rack, I do NOT tall Sonar to create tracks for all of the outputs supported by K 5.
Instead, I manually insert 1 pair or tracks for each loaded instrument, 1 audio and 1 midi, so that they are ordered like:
T1 - Audio
T2 - Midi
T3 - Audio
T4 - Midi
And then each is paired appropriately associated with each of the instruments. I do it this way because I like to that kind of order.
The process would certainly be quicker if I just told it to do it on insert of K 5, but it's really not a big deal to do time-wise.
In addition, everything is nicely named for me, which helps out a lot, and doing the above is a one-time deal per project.
I NEVER have problems with any outputs getting mixed up, or accidentally leave a bunch of unused tracks that got inserted just because the instrument supports having them.
Give it a try - I think you will find it a reasonable outcome for a reasonable amount of time, with zero problems stemming from doing it that way.
Bob Bone