The throwout bearing is what pushes against the pressure plate of the clutch. When the clutch is engaged (NOT pressing on the clutch pedal), that bearing can make loose, rattly noises. When you press the pedal to disengage the clutch, it loads up the bearing, pushing it together & it gets quieter.

The tranny shafts all have bearings, but the input shaft bearing can act almost like that. Here's one way to tell, maybe your mechanic did this...

Idle in neutral, clutch engaged (pedal NOT pressed down). It should be making the noise. As you begin pressing down the clutch pedal a T-O bearing gets quiet. A tranny shaft bearing doesn't get quiet until the shaft stops spinning, after you press the clutch pedal most of the way down.

Another way... Idle in neutral, making noise. Press the clutch pedal down suddenly & quickly. A T-O bearing gets quiet instantly, while the tranny shaft takes a couple seconds to coast to a stop.