I know that this can't be proven (or disproven), but perhaps the original concept of the MP Evangelions evolved from the Proposal document in which "the twelve strongest [Angels] ... descend from the Moon and (apparently) vaporize North America."
We know there were supposed to be 12 Harpies, although only 9 were completed in time for Third Impact [which was probably written in the story that way due to the Tree of Life / Sephiroth having only 10 focal points, with one being occupied by Eva-01.] Also, instead of descending from the Moon, they descended from flying-wing carrier airplanes into the GeoFront. It isn't completely illogical to see the parallels and imagine how this story evolution could happen.
Considering that Anno has had much more time and resources this time around for Rebuild, he may well choose a different direction for the antagonists to take. However, since it's been established that a version of the Dummy System does exist in Rebuild, Anno does the plausible option of including the Harpies in this continuity. Mind you, the Dummy System was necessary in both the TV/EoE and Rebuild continuities for the Eva-03 scenario and its impact on Shinji, but it doesn't necessarily indicate future use in the plot. Personally, I don't think that the Harpies will be in 3.0/Final, but no one really knows.