The different sound is nothing to do with the different kernel frequencies. The kernel frequency is the maximal frequency of the step signals and the OP has the same settings, same kernel freq. in Mach3 and the UCCNC and hears different sounds of the motors. Also different kernel frequencies will not cause different sounds if the running feeds are the same.

The reason for the different sounds is that Mach3 has a defective CV motion planner where the accelearions and deccelerations are often not optimal and especially the deccelerations are often higher than what you have setup in the configuration.
In the UCCNC the CV motion planner always obeys your settings and the profile is always perfectly symmetrical, this can be hear on the sound of the motors since the trajectories generated by the two system are different and therefor the sound.

An example logic analyser print of the X axis step signal with a simple G1 X0 ... X1 ... X2 movements

With Mach3:

Attachment 295098

With UCCNC:

Attachment 295100

Notice the different trajectories for the accel and deccel part in the Mach3 measurement, this has to be symmetrical if it was optimal.
With more complex paths the situation is often worse than this as this was a very simple one axis movement.