Curious myself because I just changed my Anycubic to a SKR 3 board w/ 2209 drivers .
My Y and X are also getting very hot, but prior to change I was using the Anycubic board with 2208 drivers and after hours of printing they would be warm but not hot.
I wasn’t able to adjust the settings in Klipper due to the board but in Marln I could and it was set to .8 amp but reduced hold current which I am not using now.
If I turn off Stealthchop or reduce current the motors get very noisy regardless of microsteps. The sensorless homing seems to suck with lower current as well, unreliable and not as gentle.
My Y and X are the same steppers, the Z and E are different.
I have a spare stepper that is different (original Z stepper from Anycubic) I could try if I have a pulley gear that’s not press on somewhere. I just finished the board install so I haven’t had any time to look into further but hopefully it will be a similar fix, if it can be fixed.