From a technical perspective, the knock comes from the rate of pressure rise as combustion begins. The steeper the rate, the louder the knock. (Correspondingly, the longer the delay period before the start of combustion, the steeper the rate of pressure rise, and the louder the knock).
This is why pilot injection quiets the knock so much. The pilot charge, in effect, produces the equivalent of a more shallow rate of pressure rise.
Remember, peak pressure on a compression ignition engine is much higher than spark ignition engines.
Ryan