Lilmod, according to dictionary.com the word “metaphorically” means
2.something used, or regarded as being used, to represent something else; emblem; symbol.
How is that different than how “we” mean it? You are contradicting yourself in the same sentence when you write “Everything really happened the way it is told, it just happened on a deeper metaphysical sense”. The way it is told is the literal meaning.
BTW, even Halacha can be metaphoric. The classic example is an eye for an eye. It means monetary compensation and not lex talionis.