This question was closed, and I honestly don't know why. In reading the question, I am confused as to how people thought it was not constructive. I've voted to reopen, but I want to hear the other side.
I'd like to caution us about this particular policy - it's a real thin line between closing questions like this and making most/all of character/story/plot-related questions fall into this category.
I can see closing questions that clearly ask for fan speculation, are thinly disguised rants, have no basis whatsoever in the game universe, or "what do you think?" kind of opinion solicitation, but saying "I don't understand this plot, character, or story element, did I miss something?" is a valid question as far as I'm concerned.
Just like having an answer doesn't make a question good, I'd argue that potentially not having an answer doesn't make a question bad. If a question is attracting speculative or otherwise non-authoritative answers, we can downvote and delete them, and even protect the question if needed. I don't see a problem with answering questions with "we don't know, there's no canonical answer" if that's the only authoritative answer that can be given.
How do we decide if something is a valid plot/story question or a bad "plot hole" question? There are many, many plot and story related questions that only true experts in a particular game/game series/game universe can really be knowledgeable enough to sort them. Isn't attracting and pairing these experts with intelligent questions part of our mission? When we close a question like this, we say "your expertise and enthusiasm is not the kind of contribution we value."
To the "not a real problem" argument, I'd counter that as long as we consider plot and story questions to be on-topic, not understanding plot or story has to be considered a real problem.
OrigamiRobot has suggested that the real reason this is a problem is because the question addresses a cosmetic difference in a character design, but that's not a reason to close either. Asking why Chell from Portal has weird metal strips attached to her boots and what they're for is a character question, relates to her appearance, and an interesting, good question at that.
Pushing these things to Sci-Fi & Fantasy if they are plot/story related is also problematic - what happens with games that aren't science fiction or fantasy related, or whose universes are entirely within video games? We certainly haven't been migrating any of these questions, have we spoken to the mods over at SF&F about whether or not this type of thing falls into their camp?
I think closing is the wrong tool here - it seems to be the one we prefer to bring out whenever we go "I don't like this." If a question is uninteresting, then ignore it. If it doesn't show research effort, downvote it. If it might attract poor answers from people who don't know better, flag non-answers and/or protect it. If letting valid answers to the question accumulate would be bad for the site, close it.
Here's a short list of questions that I feel are extremely similar to the one that has been closed, but are currently open.
We've got some fan-created timelines on here, and an almost purely speculative answer. Only the devs know for sure exactly how the two universes are related, right?
Who knows why the game creators titled this game the way they did? Certainly nobody who is posting answers here - they're guessing by their own admission.
Oh, the reapers' timeline doesn't match up with human evolution timeline. That's just a potential plot hole. Someone at bioware probably screwed up or didn't care about the science of evolution when making their videogame universe.
There's no real explanation in the game about why he's in prison, so this is speculative.
Tyrael's powers and his abilities don't make sense. LessPop pretty much says "this is a plot hole/plot device" in his answer.
What happened to Master Chief following the events of Halo 3? Only the devs of Halo 4 know at this point (and we didn't even know there was a Halo 4 when this was posted). Maybe he died after going into hypersleep.
Anderson's job changed between games? That's a potential plot hole. Yeah, there's an answer, but that doesn't matter, right?
Another character in Diablo 3 whose backstory doesn't make sense. These guys should form a support group. VTC.
Why are we being put through testing in Portal? Cause it's a game! Without it, there'd be no game. It's a plot device to get the story moving. The answer is "because Valve thought that would be an effective impetus to get the player going."
The Illusive Man has blue eyes because he was designed by Bioware to look that way. It's explained in the comics? Well, that's a SciFi question then.
Oh, a game hero does something that would kill a normal person and gets up and runs around like nothing happened 10 minutes later. This plot hole's practically a action movie cliche. How'd he do this? Because it's a game, and that's the pacing the developers decided on.
This is just the results of a 10-minute search for the word "plot" - I'm certain there are far more questions here just like them.
In this one particular random case, it happened to be a thing that actually meant something. I am pretty much convinced that that is an outlier at best - most of the time, these questions are just random stuff that is speculative or completely unanswerable other than by rampant theory or the developers, and well, we have close reasons for that sort of stuff.
I could ask a million zillion questions of this type. "Why is Darunia the only bearded Goron?" "Why is Mario red and Luigi green?" "Why is Wario short and round, and Waluigi tall and thin?" and so on.
This strikes me as very similar to a discussion we have had before, about why things got designed the way they did in games or gaming industry practices. Matthew Read's answer on the first question I linked sums up the point I am trying to make - more often than not, we are not going to be able to answer these sorts of questions, they're not practical, and they're not something that really fits with what we do. If we allow every speculative "why is this thing this way" sort of question, I think we will just end up with a bunch of random trivia-esque questions, which we have kinda made clear are something we don't want to attract.