The main issue here - honestly - is that we're playing a system. Systems are, by their very nature, either imperfect or so incredibly complicated you'd practically be better off just going out and live-acting the stuff - or, you know, becoming an adventurer yourself. The SR5 system says that, like, four different kinds of muscle types, control capabilities, joint flexibility, and all that sort of thing are all wrapped up in one attribute instead of four or six or ten different ones. Look at all the different types of individuals who benefit from a high Agility; let's take three Olympic ones, two of them similar and one of them different: the Sprinter, the Marathoner, and the Gymnast.
All three of these, as character archetypes, rely on high Agility - either for base running speed or for precision flexibility. The only difference between them, then, is the specific skills. All three can benefit from Natural Athlete; this is still going to leave the gymnast (who is going to need an above-average good strength anyhow, because not all those moves rely purely on AGI) with a Running pool of 6 or 7, which means a success or two. S/he doesn't have the twitch reflexes that react to the starting gun, but a gymnast does have to have quick reaction to adjust for a maneuver's differences on the fly, so I'd say that the expected Initiative is going to be the same. Does this mean an Olympic gymnast can sprint nearly as fast as an Olympic sprinter? Of course not - their high Agilities are different kinds of high agilities.
Now, both Runners obviously are going to have high Running skill, right? Only the specialization is going to be different. The sprinter is going to have a higher Strength; the Marathoner, a higher Body (in order to resist that build-up of Stun damage, y'know?) But that'll be a matter of three, maybe five dice on a sprint test. Is a Marathoner going to sprint like a Sprinter? Of course not.
The real issue lies in the fact that we can't build a reliable model of 'human' without getting into an obscene complexity of skills, stats, etc. The real issue - as it were - is that in doing what we're doing right now (which, let's face it, really is 'just be a fraggin' gamer'), we are deliberately pushing the system's edges to its breaking points. For Extreme Purposes, sure, the system is pretty busted. But for gaming purposes - in which sure, the combat turn is usually 3 seconds, but it could be 2, or it could be 5 or 10, and which we're playing cool people who can do some pretty rad things, and c'mon, roll with it, dude - since we're wanting to have fun and not get out the tape measure to measure out how far it is from the front door of the gaming store to the entry to the back room, it works, and if we let it work, we can have fun.
Push any gaming system, and it breaks; any gaming system, because it's trying to take complicated-as-hell reality and boil it down to six stat scores, a bunch of skills, and some weapons. Get granular if you absolutely have to; I'm one who feels that a certain amount of technical detail (being able to create our own guns, vehicles, and spells is very, very high on my personal Shadowrun Must-Have list) is a good thing. But yeah, even then if you push it too far ... *snap*
Hawatari - the current-day one - without Edge will hit almost 180kph at a dead sprint, sprinting every one of her actions. She has a Running skill of 3, so if she really wanted to make it worse, yeah, she could. She's meant to be faster than hell; that's been the idea behind her (fast reaction speed, fast on her feet) since day 1, and this far beyond where she started, yeah, according to the game rules she could do the 100m in under 2s if she wanted. I doubt that'll ever actually come into play (though, y'know, it might, just for shits and giggles, i.e. fun), but when you get down to it, the idea is that she's faster on her feet than almost anyone she meets, and is supposed to be. And what she's especially supposed to be - what all this is especially supposed to be - is fun.
So try not to focus too hard on how the system is clearly blatantly broken when, since it's a system, it's always going to be in error in some manner - and that the system's goal is not to perfectly represent reality, but instead to let us have fun.
Well, let us have fun and sword-swinging gymnasts who can do backflips down the track and still beat Bolt by 4.5 seconds ...