Sisrei Torah are hidden in aggadata. They are meant to be taught one-on-one with a Rebbe. See the beginning of the second perek of Chagigah ( ??? ?????? . . . ??? ????? ?????? ????? ??? ?????? ????? ??? ?? ?? ??? ??? ????? ?????)
It should also be pointed out that sometimes we might say that statement X is not meant to be taken literally because it is a figure of speech not a metaphor. E.g. hakeh es shinav.
And of course there are times where a story is literally true and is also meant as a metaphor.