Oh, I love your tags here. Even though I'm obviously not part of the editing team or within the State sphere in the slightest, it's still clear from an outsiders' perspective that Ish hates "villain wins" storylines. The endings to his videos can be bittersweet if necessary, but the villains must die and the heroes must win, and if he has to eliminate nuance or completely reverse plotlines to make that work then he will. (see: Cynikka). State 2.7 (and 1.7, to a lesser extent) is another good example of this; it had several aspects that practically seemed set up to guarantee a satisfying overthrow of the villains and win of the heroes (again, bittersweet endings notwithstanding).
I will disagree in one area, which is that I'm not sure they would've gone the antihero route with Flux. I just don't think Ish likes nuance enough for that, lol. I suspect they would've gone for the "Saps was the final, tragic loss at the very end, a symbol for how many people died even on the attackers' side (maybe the Peacekeeper attacks would've been more emphasized; make it more clear that plenty of attackers also died) "and then Flux was brought to justice after murdering Saps" (because we already know Flux would've turned himself in just for the aura) "so in the end every villain died and got what was coming to them, and even though Saps is dead, now the entire world knows he's innocent and they build statues of him, and also everyone does the typical post-war reuniting with living friends and mourning dead ones." There would be even more of a bittersweet ending, but with a heavier emphasis on the rebuilding & reconciliation afterward. The villain still dies, the heroes still win, that's all that really matters.