it's pretty implied that ellie never came out to joel in the proper sense. she lets him assume that she's into men, gives him the false satisfaction of "seeing" her "crush" on jesse, does not correct him. she's fairly confident in being gay in public for others to see and having others close to her know; so why not correct him? why dodge the topic?

was it out of fear? could it be that she never broached the topic despite being close to him in the early years because of the possibility of his reaction being negative? that she was afraid that out of all things that could force them apart (further apart after they split), him reacting badly to her being gay would be the worst?

what about at the dance? would she have been as wound up as she was if the moment hadn't been an encounter with a vicious homophobe? maybe she would've still snapped without this context, but why is she immediately on the defensive against joel after he sticks up for her?

what about the porch scene? why did she refute his question of dina being her girlfriend so insecurely, looking away, nervously and quietly stumbling over words? why isn't she mean about it? why doesn't she get defensive at the question? why did she lash out again when he expressed acceptance?

i think these scenes revolving around her queerness indicate it as such; that ellie never told joel for fear of a response, that she lets him think what he wants because that's the easiest way for it to be. then, when she's ready to face off against a homophobe, because that's the way things are, that's what she can expect, and joel defends her, she lashes out.

it's such a clear juxtaposition of support and hatred between joel and seth, and being faced with joel's acceptance is too much, makes her turn to the anger she'd been holding onto and reinforce what she thinks is true -- that she doesn't need him. and in the fallout, as her regret dawns on her, so too does the realization; he was protecting her, like always, without hesitation, over this thing she was always afraid he wouldn't accept her for.

in the porch scene, joel chooses his words wisely, and asks if dina is her girlfriend -- not "so you're gay?" or "why did you never tell me?" or "how long has this been a thing?" -- with such a casuality that it seems to throw her off. it's like ellie can hardly get the words out. she refutes the idea, fumbles for each following part of her response, is tense. she wasn't prepared for the question.

and when he finally asserts his support for her, in as explicit terms as he can, you can see ellie become emotional, touched for a moment but overcome, before she launches into the defensive again, exactly like at the dance scene -- meeting his kindness with hostility as a way to cope with her emotions.

and then, in response to her basically saying her life doesn't matter, he affirms that it does.

so he's now affirmed two things that ellie has doubted: that he accepts her being a lesbian, and that her life matters. a conflation of the two, in ellie's mind, may have come after; and after that, her olive branch.

and yeah, him affirming these things for her is fully in the context of his overwhelming parental love for her and her complex feelings about being the cure, but within a queer subtext, it means more. it's such a familiar thing to slink around loved ones and hide being gay/queer for fear of any type of response, and lying by omission in conversation just to keep that state of peace, of normalcy. ellie, with all her brutishness and bravery, falls into it like anyone else, because even while mad at him, she valued that response from him.

a lot of people seem to think that the approach to ellie's queerness is nonchalant, that it's just some unrelated thing about her, but i think that it holds more weight in the narrative that what is explicitly spelled out. it's subtle but it was a deliberate choice to place her queerness at the center of the confrontation. i think that's why ellie's relationship with dina took center stage in the story, and why so much time is devoted to just them -- because her being queer matters to her character, but in a way that perhaps only a queer person can see, analyze, and appreciate (without being blatant enough to anger certain other fans).