Supposedly the " Yamaha PIPE, INTAKE MANIFOLD Part # 5LB-13584-00-00" acts like a surge tower, sort of like the boost bottles of two-strokes years past, or what you have in your house to stop water hammer. Supposedly absords and lessens some of the positive pressure pulses coming back through intake track from intake valve slamming shut that can cause disruption of the vacuum pressure differentials that meter fuel delivery through jets and other metering orifices. It is a carburetor after all, fuel metering works on pressure differentials.
Whether having this intake manifold pipe is critical for smooth operation remains debatable. I would think that Yamaha would have deleted the expense and complication of this pipe and fitting if possible. After all this is not a Honda where elegant engineering is a corporate reward in it's own right. Profits from our TWs help fund R&D expenditures on Yamaha's other race competitive & cost competitive models.