Tears in yuri and in any other genre
Not really. Take any bullshit GL oneshot and contrast it with any shoujo bullshit oneshot. Tru tearz can be found almost universally in the first drawer, usually after or during the kissu.
It's far from a trope for a girl like Yuu to run away crying.
It's perfectly within a trope's boundaries for a girl to run away after being rejected by romantic interest. Heck, That kind of behavior is a trope in itself. It creates the unnecessary drama, and it feeds the story by providing an opportunity for creating misunderstandings (worst kind of misunderstandings - ones based in lack of communication). Besides, what i said precisely, is that it was far from her character portrayal up till this point to do that. Especially the "crying" part, if it happened.
And it's not out of character at all, because her terror of losing Touko because of her growing love for her has been a major subtext theme through the story.
It is - she did not freak out about a single thing in any of the previous chapters. Not one, not once. Her most emotional reaction till this point was her clenching her fists in unexpressed anger. If you want to believe that "love makes you do crazy things" or "act erratically", go ahead, but usually, it doesn't. And it certainly wouldn't happen here, not considering Yuu's temperament. Unless you're throwing your writing out of the window, or playing some grander narrative scheme.
After putting an end to Touko's backstory with her sister - which contrary to Yuu's reaction here WAS the gigantic cliché
It really is like we're reading different comics. Or maybe it is that we want to read different comics. Doesn't really matter though.
about the dark-haired girl losing a family member and having a ludicrously melancholy* character arc spinning out of that
...yeah. You know, if the only thing you care about here is "romance", you don't have to stay. There are probably hundreds of other titles you can read. And i really don't get that obsession with hair colors.
*what? There's been nothing melancholic about that arc.
I'm happy Nakani Nio is now able to leave that trope-y nonsense behind
She was, up till now. For better or worse, it played deconstruction on some aspects of usual romance presentation and scorned selectively at its cliches. What she did here (specifically in this chapter), or what it at least looks like for now, is the exact opposite of that.
and is writing at her strongest in this chapter.
...just no. Just because she's reenacting something familiar, doesn't make it strong. What set this title apart from Yuri Hime forgettable crap was diversification of themes, and putting small personal spins on each of them. Regressing towards the mean isn't awful per se, but it isn't great either - i hope she isn't running out of ideas.