I just had a huge déjà vu experience reading this post. It sounds *exactly* like my DS at and about that age. Also an "unholy mix" and 2E. FWIW, it's probably a good thing you see the "E" in this, because my interpretation (then, not now that he's nearly 13) was always G not E.
I understand the concern and frustration you feel, but I'd reframe it in terms of *density* and try to see it as a difference in perception. I adore your son's answers re: difference. Such an ambiguous word! He's out of the box, and that's okay, just have to teach him what is "usually meant."
My DS is also a literal thinker but once he understands an idiom, he usually gets a big kick out of word-play on it.
