I think you assume the story is just Fallout with ponies in it, like a script copy or something. Lets quickly go over a few things first:
Problem 1 - If you take a movie script writer and have them write for a game, it'll usually be terrible because you can't mix media like that, the methods of game design and linear storytelling are very different, books tend to have the largest amount of character dialogue while games typically have fewer words spoken by the characters per minute than tv shows. Then there's pacing differences, themes that work on one but not the other...
Problem 2A - A copied script would just lead to fans of both hating the end product, if you could just copy the dialogue from a particular game session over to a story and change the names a bit, you'd get called out on it immediately.
Problem 2B - Why would the spinoff fanfictions be spinoffs of Fallout:Equestria rather than just from Fallout if it was a copy? Why would there be this much fan content, even.
So, I think that the odds of a carbon copy getting this much attention is very low.
Now, lets assume that the fans of the story not only really enjoy watching the show, but also are fans of the game, which isn't unusual since it was one of the most popular games... ever, I think. We're going to assume this because there's a few barriers to get through:
Barrier 1: Crossover fanworks tend to need the audience to be aware of both settings in order to get much of the humor/setting references, the worst cases fail to describe characters physical features or the features of important landmarks, instead relying on the original works for support. This is not a flaw, reading fanworks that describe Twilight Sparkle in full detail back to back would be a living hell. Due to this requirement, many stories usually drop the ball when describing things and so readers have come to avoid these sorts of stories on sight.
Barrier 2: Some people don't want to expose themselves to certain media for one reason or another. Since watching MLP requires adult males develop a thick skin, the only audience you're going to get are people who are willing to admit they enjoy the show. They might not admit it to friends, but they have to admit it to themselves, which is the first and hardest barrier for many people. Same goes with the Fallout games, though the reasons might be different. In the end, not everything is for everyone, which is why this barrier works both ways.
Barrier 3: Some people only enjoy arguing against doing what other people do. Not unique, I'd like to point out that many ancient mythology stories feature parents casting out their children, the children returning one day and in the end defeating their parents or completing their tasks and gaining the throne or whatever. Cycle of life stuff. Tale as old as time. Still, kinda annoying when someone feels superior for not living life to the fullest. As a kid I used to dread dying too early in life and missing out on all kinds of future inventions and shows and books, and then I realized I was missing out on all those things in the present just by avoiding things that seemed pointlessly popular. This might be true for major industries where popularity is bought, but the internet is powered by word of mouth, and if cat pictures have proven anything it's that word of mouth brings many good things that advertising promises but never delivers on. So, if too many people say something's good, imagine that they might be right?
So, fans of the show and fans of the game somehow get through these three barriers and can now form opinions on it. We're assuming the fans are mostly coming over from watching the show due to the story being on Fimfiction, though the other way around is possible. If the fans are on the MLP side of things, then that means they can hold the story to some of the standards of the show, regarding quality.
Upvotes and likes and view counts are useful tools, they let us know if a story does a good job, but they also let us compare these stories to other stories written at the same time. If the story is higher than average then, odds are, it's also higher than average quality, regardless of the actual numbers involved.
If it looks like a duck, swims like a duck, flies like a duck, and quacks like a duck, it's probably a duck.
If a crossover story generates a large audience and massive amounts of fan content with several thousand views, odds are it's good.
If the idea in your head about what the story is doesn't come close to meeting all these requirements then odds are they're opinions formed from nothing, masquerading as something more substantial. Okay, so you don't like a story you've never read based on a game you played for five minutes, that's fair. Opinions are pretty cheap, after all, have as many as you like. As someone who played the game for years, watched the show on weekends on repeat with friends for years, and read the story a few times over, my personal opinion is that it's a good story, I wish there were more professional works like it, I wish the games had as much emotional impact as it, and for a grimdark story this one does a great job of keeping the characters in character, even if Twilight and the others only infrequently appear.