My thoughts were to keep the pin variable consistant, to what its purpose has been in the past. A third variable would indicate that we were doing something different than what we had done in the past.
I have programmed other Atmel chips on their platform and I could have sworn that I set output pullups... I might be wrong, but it does seem that we can't do it on the mega 168/328. Sorry for the confussion but I was quite sure they could be set.
Because the outputs can't be set it may just make more sense to set up the function for the 2 variable inputs as suggested.