As I said, it's a personal preference thing.
I don't have numbers on a performance comparison -I have operated both ways, and the load time for me is quite a bit better with a single instance of Kontakt then it is with 3 or more instances.
If it is working how you want it to, then set up the tracks in whatever manner gets you there.
If you are on the other hand having slow load times when using multiple instances of Kontakt, then I would suggest that you give it a try on loading multiple instruments and doing track assignments for instruments 2 and 3, (assuming there that you would have opted to create 1 instrument track on the initial load of Kontakt).
It is my opinion that it would take less time - for the single time you would have to do it - to set up the multiple instruments, run the batch function to set up internal routing, and create.assign tracks - then it would to wait for 3 instances of Kontakt to load, more or less just to avoid doing some rudimentary track assignments.
It is your choice -test out both ways or don't - your choice - your results. You expressed some dis-satisfaction with the load times, and I would think that would motivate you to try to tweak what you are doing to see if it improves performance.
Bob Bone