The difference is more likely the individual drives, and not the software in use, particularly if you perform the same tasks on both Macs.
The HDDs, being mechanical devices, will have minor physical differences due to manufacturing tolerances (motor speed, bearing clearances, etc), so one drive may turn out to be noisier than another identical drive.
The only fix would be to replace the noisier drive. Be aware that you may replace with one more (or less) noisy. Just part of life with mechanical devices. Sometimes you get lucky, and the spinning drive may be almost inaudible.
If you truly want no noise, then replace the spinning component of the fusion drive with an SSD.