Think about it like this:
Take a top down view of the engine/jackshaft arrangement. You have two wobble bearing supporting a jackshaft that in no way, shape or form resembles the quality of a Yamaha shaft. Now you have a 200+ hp motor pulling on the cantilevered end of the shaft. There is nothing to keep the jackshaft from bowing in the middle between the two bearings and knocking the secondary out of parallel with the primary under load. Your parallelism can be dead nuts on at rest, but will not be when the sled is going down the trail or climbing a hill. Cat fixed the center to center on this sled, but as a result, gave us a sled where the parallelism can change substantially depending upon how the production tolerances of parts line up.
With the TCL left in place, the parallelism of the primary can change by 40 thou + depending upon how far the mag side rocks forward under load. You can test this by putting gauges on the primary in relationship to the secondary and push the mag side forward.
Again, there is a reason Cat dropped the TCL like a hot potato at the very first opportunity (7000/Viper) and it is likely Yamaha insisted upon the change.
Cats new secondary will help by dissipating heat, but will not go to the root source of the heat. I would highly recommend that anyone who has not invested in aftermarket clutch to get the new Cat clutch.