While it's true that the average man is more attracted to looks than to status, and the average woman is more attracted to status than to looks, be careful not to over-generalize these preferences. Harry doesn't seem to mind, for instance, that Hermione is plain looking, and admires her intelligence, while the average man prefers beautiful women noticeably less intelligent than he is. Hermione isn't particularly attracted to high status men in canon (she picked Ron over Viktor Krum, for chrissakes), and there's no indication that she's different in MoR. Neither of them fit the personality profiles that the PUA community has studied most heavily, which I've heard described as "extroverted young women of average intelligence" and... well, I haven't been informed about the type of men specifically, but I'll hazard a guess that they're not like MoR Harry. So PUA models of interaction between the sexes wouldn't give you very reliable intuitions about how Hermione and Harry should act towards one another. Never mind that they're prepubescent and applying any adult models of interaction that were developed with sexual relations in mind to them seems kind of creepy in the first place. "Relationship" aside, they're mostly friends at this point.

I mean, I agree with you that Harry's apology was rather embarrassing, but that was because it wasn't warranted by the circumstances. If he'd actually done something worthy of an abject apology to Hermione, then he should be giving one, not restraining himself in order to protect his dominance over her.