That wasn't aimed at anyone specific, you know, just like... people make such lengthy arguments over minutiae and cite single sentences as pivotal bits of evidence for a given interpretation, drag around interviews with Yoshi-P for easy citation, etc. I'm just not sure where some people find the time to play, considering. Keep it succinct, y'know? (I gots ta get my Archfiend Attire before season's end in a few weeks, one rank a day oughta do it. Right?)
Anyway...
Even within that selfsame cutscene we have Venat talking about how horrible what she's done is ("I breathe fire and torment. I birth a world of suffering to mire and plague."), and ultimately what Y'shtola is saying there is that they should make her suffering and sacrifices (which include her innocence, life, and soul, as well as ~12,500 years of physical and emotional agony in solitude) meaningful. Once the truth is out nobody is under illusions that Venat's hands aren't stained with blood and sin, but it happened, they wouldn't exist otherwise, and all they can do is make the best of it.
Dynamis was a largely unknown force in the universe even amongst Hermes' closest colleagues. Even Venat, likely the most worldy of the Ancients, had heard little about it. Yes, theoretically they could have had some other supergenius researcher create an Anti-Meteion... somehow... I don't know how, given what we know about her, but sure let's go with that. It's just as conceivable they wouldn't though, particularly given no small number of them were offing themselves in Zodiark's name out of regressive nostalgia after the Final Days.
And not all of the Ancients were as powerful or talented as Emet-Selch, or the Convocation, etc. Erichthonios shows us that not all of the Ancients could "create anything with a snap of their fingers," and they still worked on equivalent exchange.
Um... after A Realm Reborn, all of the villains have been given sympathetic backstories (except Thordan, maybe), even if it was acknowledged they ultimately needed to be put down. Conversely even before Legacy ended the protagonists were doing questionable things, like Louisoix summoning demi-primal incarnations of the Twelve in a desperate gamble to stop the Calamity. The antagonists having "good" reasons for their actions and the protagonists doing shady things is... absolutely not something new in Shadowbringers or Endwalker. At least not by my reckoning.
Also are you seriously saying people who liked Endwalker are braindead? That's kind of funny, because I've seen arguments that go in the complete opposite direction suggesting they're overthinking things (i.e. the philosophical underpinnings). So which is it? Cuz if it's the former just let me enjoy my mindless entertainment; if it's the latter I'll gladly elucidate the existentialist philosophy behind the story. Maybe even throw in character analysis of Moxxi's Heist of the Handsome Jackpot, the only piece of Borderlands 3 content worth a damn story-wise, just for fun.
Lemme know, ayy!