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I think I get Hazel's saying. When the goddesses departed for the Heavens in the Great Deku Story they formed the Triforce which in turn fused all the goddesses together and they as one became the Goddess of Time.

Adding more insight to Michael's PoV(point of view) maybe the this supposed goddess was their at the creation but had no significance in the Hylian creation legend so she was never mentioned which is why we only know of 3 goddesses.