Is it possible to use digital GPIO pull up and pull down functionality on a pin that is connected to APORT on EFM32PG1?

Yes, the pull up and pull down functionality of the GPIO block can be used.  This will enable the input buffer and may cause increased current consumption if both transistors of the input buffer are activated by an intermediate signal.  This will also enable over voltage tolerance circuitry which may cause a slight distortion (only noticeable at 12 bits of precision) and a slight increase in settling time.