I never said either of those things. I said it was implied narratively and think it's a horrible narrative mistake.
Undoing all the progress the characters make is lame, uncreative and hurts your ability to be involved in the story. It's the same thing when they bring Palpatine back in Star Wars or how the Ninja War arc is the worst part of Naruto because they just bring all the villains back from the dead to fight them all a second time. Even in the Zelda example you gave, Ganon ALWAYS coming back is something that makes that Zelda games feel weaker and if you treat them all as a single narrative it's monotonous and stale.
It's like... I don't care now. I've already seen this world overcome racism why do I wanna see it a second time? And are they just gonna do the same thing yet again at the end of this series for G6? Apparently you'd think that'd be a great decision because 'peace cannot last! KEK!'
And I suppose in a nihilistic sense you're probably right with your 'we all gonna die everything you do will crumble it's all for nothing, bro!' mentality, but... that's not what I come to MLP for. I watched G4 because it's one of the very few happy shows that remained on television where friendship is magic and good can overcome problems. Turning the message into 'Racism will always win!' and 'Everyone you love is dead LOL deal with it bitch!' are attitudes that take that feeling away from me.
Don't get me wrong, I'll watch dark and nihilistic stuff like Rick and Morty or whatever, I just don't think EVERY show ever needs to lean into it.