What is the difference between clamping a input signal at X volts and clamping a input signal by X volts
We use by to show how something is done.

We use at to show some point of reference like a voltage or current or a plateau after a certain point in time where the signal has positive edge ( or in the general sense at some location)
Clamps are used to limit voltage swing in some direction relative to some Voltage Source/Sink or Ground.


The polarity of the diode switch and whether it is AC or DC coupled serves totally different purposes as well as where the other end is connected. (Polarity and Voltage matters)  Here we say clamped AT some voltage like 0V (GND) for restoring DC to a negative peak, or Vcc for positive clamping above Vcc for further rectifying a low side PWM switch to create a boost voltage above Vcc for a high side Nch FET gate voltage.
When no convenient voltage is available , we might say clamped BY when using a TVS, MOV or Zener to limit the voltage swing, BY some active device with an independent voltage limit.  where we mean clamped AT some value AND polarity at some point in time ( Vpeak or sync edge)  BY some device.
If you just said clamped by 100V then you must specify how and with what or the criteria to choose that.
Using diodes or synchronous pulsed an AC coupled switch one can clamp during the middle of waveform like sync pedestal after neg. sync tip on a video using C coupled and a one shot switch to charge the cap by a FET or transistor switch to ground.  Here again the signal is clamped AT some voltage BY some device and BY some trigger method.  This is also called   DC restorer circuit for Black Level.
Short Answer:
BY must imply a  method or a device not the result like V or I.