What you are describing is "gear clack". And they all have it to some degree. It is exacerbated by cylinders that don't fire with same power as others. Proper carb balance and fine tuning helps.
Here's why:
The trans main gears are all meshed, even if not engaged for power flow by the gear dogs. If during idle the crank speed changes, the gear teeth change their contact face alignment front to back which causes a "clack" sound. And there is a lot of them inside the case. Only when the crank turns smoothly is the play between the gear teeth not noticeable. Higher revs, and a change in gear box moving part inertia from the clutch basket and discs alter the sound frequency and intensity.
As the trans parts wear, the tooth to tooth gap increases magnifying clack or rattle sound.
Most CB550's will make this sound unless the pistons all fire with equal intensity. Otherwise the minute changes in crank speed from uneven firing will make the trans gears clack at idle.
If all the cylinders have the same exact compression, and they are all fed identical charges of fuel and air, then the crank rotation is smooth between firings, and trans and/or clutch basket part don't change their orientation with their mated parts, producing no noise.
I don't like the gear clack so I find a tune or RPM where it is avoided when cylinders wear unevenly. But, I will vacuum balance the carbs, and then twiddle the air or IMS screws to minimize the clacking. All to get each cylinder to fire with the same strength as the others during idle firing sequence.
Cheers,
