Usually, when an aircraft have its own throttle calibration, that means your MSFS Control Sensitvity curve for your axis needs to be linear with everything at 0% except for response/reaction which needs to be at 100%.
Then as long as your throttle is linear, then the ATR EFB can finally calibrate it correctly by reading the correct values from your throttle. But that means you need to manually calibrate the throttle via the ATR EFB “After” you set your control sensitivity to linear. If you calibrate the ATR EFB using your old sensitivity curve and not recalibrate it again, then it’ll still gonna get messed up.