The TO bearing serves as the interface between the clutch fork and the diaphragm of the clutch pressure plate. One portion of the bearing is stationary while the other is free to rotate as it makes contact with the diaphragm. The rotating portion is what rattles if the bearing is poorly designed, if it wears out, or both. When the clutch pedal is pressed, the bearing is pressed up against the diaphragm (to release pressure on the clutch disc) which stops the rattling.

As mentioned above, the input shaft bearing can also make some noise. These are quirks common to all manual trans cars. Some just use "quieter" parts than others.