A victory of the villain and a total destruction of the world is something that most shows don't do.

It has nothing to with it if the show is a show that is watched by kids also, it's just something very unusual for tv shows in general, because most creators like it when the good win at the end.

For the creators of MLP: FiM, I also don't think that they will do that, at least not permanently, even when they have the balls to do so, but a temporary victory of a villain, that has to be stopped with a second plan then, because the first one failed or simply giving them a very hard time with defeating the villain instead of a quick "Taste the rainbow, motherfucker!" (which is even not possible anymore, now that they don't have the elements anymore, so, real fights are come eventually!) is something they would definitely do.

The second one is also something they already did, with Discord manipulating them and turn them into the opposites of their true personalities, to prevent them from using the elements in the season 2 opener.

That's also the reason why I don't buy it, that he is still evil, he is a trickster that manipulates his enemies and it's not unlikely for a trickster villain to make the protagonists think he's on their side.

My secondary theory about the containment (althought it didn't come up myself with it, this was inspired by a comment on EQD) is, that the box contains something he needs and that the Mane Six should get it out for him, which is the reason why he holds himself back for now.

To advance that, it's also part of this theory of mine, that the containment of the box is something that shouldn't get out at all, because it's dangerous and that the Tree of Harmony simply gave the box to them so they will guard it.

When you listen closely, you recognize that he seems to talk when he gives the box and after several watchings of the opener I have figured out he says "Don't open it!".

But his voice is scratchy and not very understandable, because Discord used his chaos magic to manipulate the voice of the tree, so that they couldn't understand him.