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"A lot of it is pretty dang hit-you-over-the-head-with-a-stick obviously metaphorical"Origen: "[if scripture was purely literal] we would not certainly believe, when thus possessing the meaning of Scripture in a continuous series, that anything else was contained in it save what was indicated on the surface; so for that reason divine wisdom took care that certain stumbling-blocks, or interruptions, to the historical meaning should take place, by the introduction into the midst (of the narrative) of certain impossibilities and incongruities; that in this way the very interruption of the narrative might, as by the interposition of a bolt, present an obstacle to the reader, whereby he might refuse to acknowledge the way which conducts to the ordinary meaning; and being thus excluded and debarred from it, we might be recalled to the beginning of another way, in order that, by entering upon a narrow path, and passing to a loftier and more sublime road, he might lay open the immense breadth of divine wisdom. This, however, must not be unnoted by us, that as the chief object of the Holy Spirit is to preserve the coherence of the spiritual meaning, either in those things which ought to be done or which have been already performed, if He anywhere finds that those events which, according to the history, took place, can be adapted to a spiritual meaning, He composed a texture of both kinds in one style of narration, always concealing the hidden meaning more deeply; but where the historical narrative could not be made appropriate to the spiritual coherence of the occurrences, He inserted sometimes certain things which either did not take place or could not take place; sometimes also what might happen, but what did not: and He does this at one time in a few words, which, taken in their “bodily” meaning, seem incapable of containing truth, and at another by the insertion of many." - http://www.ccel.org/ccel/schaff/anf04.vi.v.v.i.html section 15
Origen was one of the foremost Christian scholars of the 2nd-3rd century. This was the predominant approach Christians took to scripture until 19th century America, when literalism took over -- for a short time.
Of particular note, the earliest parts of Genesis would have been obviously metaphorical to any of the early readers... because they blatantly undermine the Egyptian creation stories. They take the most significant Egyptian gods and describe them as mere objects (even the sun and moon aren't named -- they're just "lights".) They take the most significant elements of the Egyptian stories and turn them around, twist them up on themselves, and use them to express how Yahweh is different from Horus, Isis, and the rest. It's like the way Shrek takes common tropes from Cinderella-type movies and turns them on their head, only serious instead of comedic.