I think that is a horrible statement. Yes, the GM is the final say, but both the players and the GM have to work in the same world. They have to be playing by the same set of rules that govern said world. It is one thing to be working with houserules or even invoking fiat, but if the GM is going to say that a specific aspect of the world officially operates in a certain way they should be able to not only back that up, but be able to tell or show the player where that ruling comes from so that the player can further educate themselves.
The rules govern the world, and the world is what makes it ShadowRun. I don't think I could stay in a game where the GM feels using the rules is "nice when you can."
My guess is you're not a GM. What's horrible is when you're a new GM, the group is in the middle of an exciting battle and your sammy fires a grenade down a hall. You're not up on your scatter or chunky salsa rules so you say "I'm not gonna worry about it right now." but the player whines and wants you to look it up, which you know will bog things down, and all he's doing is hoping it will get him a few more boxes of damage. Or a car chase breaks out, and knowing that those rules are a ridiculous mess (at least in 4E) and you haven't once looked at them, you wing it and the player says "No no no no, I know that's not how it works" (but they can't tell you how it works either). Circumstances like that, all the other players can do is roll their eyes and pick up their phones. That's horrible.
I never said GM doesn't play by the same rules he improvs on the players. You 100% projected that onto my statement. And sorry rules don't govern the world, the GM does. Absolutely the rules are a great guide for the GM the majority of the time, but if the rules get in the way of the story, sorry but the rules gotta take a back seat. And the rules governing the world do not make Shadowrun, not even the Meta-plot makes Shadowrun, the dudes/dudettes sitting around the table do.
Consistency is important, but if the players understand you don't know how something works at that time, but you'll look it up and "do it right" once you've had a chance to get a grasp on it, what's the harm? Honestly, please answer that question. Even if you change it down the road, what exactly has been lost (and how was it worth more than the time gained at the table actually doing things)?