The thrust lapse rate in alternate mode is not the same as it is in normal mode. In simple English, that means that the change in N1 (and hence thrust) with forward speed and changing altitude isn't the same in alternate mode.
The penalties for EPR engine in alternate mode tend to be greater than N1 rated engines, because not only do you have different lapse rates during takeoff there is greater uncertainty in thrust when setting power on an EPR engine using N1.