I think that the point is that you need a base thread frequency high enough to handle the maximum required step rate, but there isn't that much to be gained from having it much higher, and the disadvantage is that there is quite a waste of CPU time.
So Stepconf uses 100,000 if 100,000 is short enough to reach the required axis speeds.
If you were to increase the axis speeds in stepconf then I think that you would eventually see the base period reduce.
That said, there is _something_ to be said for a shorter than necessary base period. Consider the case where you are stepping every base thread period at 100,000ns, ie 10kHz. The next speed down without dithering is 5khz, ie stepping every second period. This is partly why Mesa and Pico cards can appear smoother, they have a base clock in the MHz range, and so can make fractional changes.. 10kHz - 10.001kHz...10.002kHz etc.
