I'm rather certain you're wrong in that assumption, Ferahgo - though the guesswork is good.
RahXephon is an original work by Studio Bones, like was the case with N.G.Evangelion and A Vision of Escaflowne. Or so I liked to believe from everything, and if my memory serves me right the anime came before any manga adaptation.
In searching for some proof or indications, I did fish out this Anime News Network entry profiling the manga as an "alternate re-telling" of the anime:
http://www.animenewsnetwork.com/encyclopedia/manga.php?id=3390
Anonymous in comment 1's theory seems plausible:)
Either way, I haven't read the manga, so I can't make an argument on it's merits. I did like the anime a lot, despite it's influence from Evangelion.