OP, thank you for posting because I know exactly what you mean! My DS is only 15, but he's always been a year or so ahead of all the standard age related behaviour, and I am in the same position than you, feel stuck and I too worry about how our relationship is evolving.
At the moment, I am not managing to find the right balance. Like your DS, if I pick him up on anything, I get a defensive response, no matter how nicely I ask/mention it. I ask very little of him, but the moment I open my mouth to ask for something, I get that 'yeah, I know, no need to repeat etc... , then he doesn't act on it even if I give him time to do so. So I'm left with ignoring or becoming more assertive.
When I become more assertive, either raise my voice to make a point, or calmly say that I'll have to enforce a consequence, he gets angry and then depressed and withdrawn. If I don't say anything, he doesn't self motivate himself to put act on the few things he needs to do.
When I end up getting frustrated and do it for him (mainly cleaning his room that he lets become a complete pig sty), he then thanks me a lot, admits he doesn't like when his room gets so bad, promise to work with me, say that he will give it half an hour every Saturday and I can punish him in any way if he doesn't do it, etc..... Then I gently remind him of the agreement and we are back to the 'yeah, I know, whatever' and we are back to square 1.
Part of me thinks it's just a phase, but part of me worry it isn't because it seems to be gradually getting worse and I feel that a gap is growing between us. Like you, he does well at school and has a very good social life. He is a good kid, hasn't got in any trouble at all so far, not interested in drinking, comes home when he says he will and his teachers love him, but he just always seems so miserable at home, it's unnerving.