The sound is caused by the drive head hitting the backstop. By default trackdisk.device periodically steps it inwards, causing it to hit the backstop every time.
From version 33.7 of trackdisk.device an alternative method is available that steps the head out, and then in again alternately. That way it doesn't hit anything. Other utilities that do this either make use of that feature or patch trackdisk.device to add it.
From the trackdisk.device source code:
* ;------ Step the drive. We will recalibrate it eventually
* ;------ anyway, so don't worry about where it is.
* ;------ if noclickstart flag is set, always step out.
* ;------ to save space, clear it then change it to set it.
* ;------ D3 is a flag to tell if I changed direction.
MOVEQ #0,d3 ; assume changed (d3=0)
BCLR #CIAB_DSKDIREC,TDU_6522(A3) ; will get changed!
SNE d3 ; d3=1 if bit was 1