Hi,
Yes, I'm familiar with that issue from the 3.0L and 2.7L V6 TDI engines, and as you suspect, it's due to the pre-injection.
"In my case, this issue occurs sporadically under varying load conditions and at different temperatures (both coolant and ambient temperatures)."
You can easily view the pre-injection dosage values in the measurement data sheets. I don't know the exact specifications for your engine right now.
When the engine is misfiring, you can see that the pre-injection is being set to 0.0. If the engine suddenly becomes quieter, the measured value will change to a positive value.
However, I haven't yet been able to determine exactly which sensors, data, or measurements are being used to control it.
I have a faulty fuel temperature sensor (short circuit/open circuit without an error code

because, in case of failure, the engine temperature is immediately used as a substitute).
I switched and got a slight improvement (nail biting occurs less frequently).
I also replaced the coolant temperature sensor three months later, which slightly reduced fuel consumption, but didn't affect the knocking sound.
I also had the LMM (likely referring to a mass airflow meter) replaced due to mileage, which the automatic transmission appreciated. However, the knocking sound hasn't changed.
Now I'm focusing on the rail pressure sensor or the rail pressure regulator, but it still needs some more data logs and test drives for proper diagnosis.
You could check the rail pressure on your car to see how it behaves when it's misfiring, and then when it stops, to see if it fluctuates, increases, or decreases, etc.
That's all based on my experiences so far.
Regards, Mpire.