Updated to marlin 2.0.1 now the stepper started to make a lot of noise. Downgraded to 2.0.X and the printer is silent again... ?
I noticed this as well and to be honest it was right after my mainboard swap so I was well use to what SpreadCycle sounded like after many a nights trying to sleep through it. A SKR mini e3 running in SpreadCycle whether it be from the hybrid threshold or not screaches louder then the stock Ender 3 Pro firmware and board ever did. I personally raised
#define Z_HYBRID_THRESHOLD 10
to 100 and this eliminated the most annoying/ scary part which was during homing the z axis. It was screaching loud enough I thought something was wrong with a threshold of 10. I honestly felt then and now especially like something else is set wrong even in SpreadCycle the ender 3's stock stepper motors shouldn't screach that loud.
After changing the z threshold I now only notice SpreadCycle kick in while probing or when the head moves from one object to another but now seeing as I'm not the only one who thought it was screaching I think its worth looking into!