What effect does tropopause entry have on the FMGC?
It adjusts the FMGC temperature model to account for non-standard temperature. This will have the effect of improving performance predictions by having a more accurate temperature model.  

The FMGC uses a temperature model based on the International Standard Atmosphere (ISA). The ISA is based on a sea-level temperature of 15 deg C. In the model, temperature decreases with altitude at a rate of 1.98 deg C/1000 feet up to the tropopause. Above the Tropopause, the temperature is a constant -56.5 deg C.  

Updating the tropopause as well as entering the cruise altitude/temperature will adjust the temperature model closer to actual and thus improve predictions. Not entering either value will result in predictions using the ISA model which will reduce the accuracy of predictions (except in the off chance the actual weather matches the ISA.)