I think some part of Baltar, or something he developed/discovered is what teh cylons use for their "projection". So, in a sense, they will come to realize that Baltar is their God.
Probably not quite that literally, but it wouldn't surprise me to see one of the 2 sides (Cylons or Baltar) come to this realization. Didn't the 6 in his brain already announced she was an angel?
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