1) A general desire for fairness. There are a lot more places where fanfic is posted than just AO3 and FFN. AO3 is the archive where Yuletide is run, so it should obviously be used to determine eligibility. FFN is an unrelated archive and should be treated like other non-AO3 archives, i.e. ignored for the purposes of Yuletide.
2) Participants often screw up when counting fic in their fandoms. The most common screw ups when counting fic on AO3 are to forget to select Complete or 1000+ words or in English, all mistakes which would make the fandom seem bigger than it really is. Accordingly, it's most likely that a nominator who screwed up their AO3 counting would nonetheless nominate an eligible fandom.
The most common screw ups when counting fic on FFN include the AO3 common mistakes as well as forgetting to check crossovers and forgetting to include Mature works, both mistakes which would make the fandom seem smaller than it really is. Accordingly, a nominator who screws up their FFN counting is much more likely to nominate an ineligible fandom and hence to waste their nomination slot.
Re: FFN
2) Participants often screw up when counting fic in their fandoms. The most common screw ups when counting fic on AO3 are to forget to select Complete or 1000+ words or in English, all mistakes which would make the fandom seem bigger than it really is. Accordingly, it's most likely that a nominator who screwed up their AO3 counting would nonetheless nominate an eligible fandom.
The most common screw ups when counting fic on FFN include the AO3 common mistakes as well as forgetting to check crossovers and forgetting to include Mature works, both mistakes which would make the fandom seem smaller than it really is. Accordingly, a nominator who screws up their FFN counting is much more likely to nominate an ineligible fandom and hence to waste their nomination slot.