I would have thought that the reputation from meta.stackexchange and possibly the Stack Exchange sites would count towards your "score" on Area 51, particularly when an existing SE 1.0 user is supporting a proposal for a new site on that subject as they've already demonstrated their commitment to the site.
As I understand it the idea of the score is to give a measure of your involvement and likely contribution towards a site (though I didn't see this mentioned in the FAQ has this changed?), so it seems to me that existing users should have some recognition of their involvement. I see a lot of active meta.stackexchange users that don't have much SOFU rep supporting sites, these are likely to be some of the people that will contribute the most to those new sites.
I understand from this answer that the sites may eventually be merged, but in the meantime shouldn't reputation from that site count?