Hi JakeTwist, nice to meet you. I looked up the post you mentioned, and I see that I answered it, only I addressed my answer to J. Did you used to be J, or did I make a mistake? If so, I apologize. Either way, glad you're here. Your post is interesting.
I think the "sometimes I wish you so much" scene may be an example of those permanently unreconciled enigmas you mention, where you just have to interpret it the way that makes most sense to you, or the way you'd most like to think of it.
I am happy to make excuses for Ennis in almost every one of his nonresponsive scenes, because they're usually accompanied by expressive nonverbal language. But this one really does bother me. I would love it if he'd said "I know what you mean" -- it wouldn't be so demonstrative as to be out of character, but it wouldn't have left Jack's big statement just hanging there unrequited.
However, I do tend to lean toward the "he feels guilty about what he has to say tomorrow" interpretation. For one thing, he clearly does feel guilty about it -- he is all nervous when he brings it up, and he waits til the last possible second to do so.
Also, I can't imagine what else he'd be thinking except that he does know what Jack means. Not "Really? That's funny, cause I sure don't miss you." No. He missed Jack like crazy during their four years apart. Sixteen years later, he has trained himself to stand it ... except that the very next morning, he confesses that he can't stand it no more. And there's another enigmatic line in itself. But I think that in view of the fact that "If you can't fix it, you've gotta stand it" is such a significant theme in the movie (and, for that matter, the story), it makes sense to pay attention when the word comes up.
So I guess, stretching as hard as I can to defend Ennis, the "stand it" part may be another part of the reason he remains silent. He's thinking, "Uh-oh, Jack can hardly stand it, but he's got to -- I have to skip August and I can't fix that." So he turns away, looking troubled.