the diesel noise is caused by the ignition delay of the fuel and depends on the amount of fuel injected before actual ignition. If you can get a lot in before it begins to burn, you'll get a rapid pressure rise as it all suddenly goes off together, which is the cause of the knocking/rattling sound.
pilot injections, rate-shaping, or whatever-you-want-to-call-it that the electronically controlled injectors do are all designed to limit the amount of fuel injected prior to ignition.
Having said that, not much of this has anything to do with torsional harmonics, hymomics or any other imagined figment that the propeller sees. It's the compression ratio that pretty much dictates the torque amplitude for a given load/power level