There are many, many problems with the ending; its ambiguity is one of the smaller ones. The language they use suggests that the altered ending will be the existing ending with additional exposition regarding the mechanics of the deus ex machina. That's not a fix at all; they're still left with [spoiler]introducing an uninteresting new character after the climax, who assigns an unforeshadowed new motivation to the villains, which is based on an idea that the story has already demonstrated to be false the few times it came up[/spoiler]. And that's in the best case, where they do "clarify" [spoiler]what happens to your crew, how fucked everything is, how you get back to earth in Destroy, why Destroy carries the drawbacks it does, what the fuck Synthesis even means, and what's the deal with that goddamned kid[/spoiler]. I can't imagine any explanation for some of those without retconning them, let alone satisfying ones.
The ending is bad as much for what it does as what it doesn't do. I'm hoping that this "clarify" nonsense is just amateurish PR desperately trying to avoid saying that what they're trying to fix is a problem.