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First of all, that's not universal. In Hong-Kong, according to Runner Havens, runners are expected to pay the Triad boss just like any other gangs (and it makes perfect sense in the HK underground).
Smart runners will have all kinds of underworld contacts. It's a useful thing to have. And if the players decide that they have a "business arrangement" with a criminal organization, and represent that by giving them money from time to time, that's fine too.
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- The concept of "deniable asset". If a runner can be traced back to a mafia, corps could retallliate against the mafia, which is some order of magnitude different from the cops trying to stop a car thief ring. Besides, while the mafia can use their influence to protect car thieves from police or to expose them if they aren't cooperative, they won't have so much leverage with corps and runners. More often than not, the corp won't be interested in catching the runners once the run is over.
Some criminal groups do have corporate ties. They certainly do in the real world. And even in Shadowrun, some corps are practically known for it: IIRC, Mitsuhama has several Yakuza bosses on their Board.
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- Mafias are territorial. They control racket on their turf. A runner might have safe-houses there, and will pay adequate protection for them, but that's it. Unless we're talking about low-key runners who only take job inside a neighborhood. In that case, I guess they won't be exempt from the mafia tax.
It's not nearly that clear cut.
First of all, when you say "mafias", you mean organized crime groups, only one of which is known as the Mafia. I already mentioned the Yakuza, and there's the Triads/Tongs, various street gangs, the Seoulpula Rings in Shadowrun, and many others.
Second, they don't always control geographic "turf". Sometimes, they control rackets: the Mafia might control shipping and gambling, the Triads handle opium and knock off products, the Yakuza does prostitution and white collar blackmail, and so on. They can be scattered all over the city, but remain under one groups control.
Third, even when they do own areas, those areas can be wide spread. For example, the Triads/Tongs exist in many forms, ranging from perfectly legal "Benevolence Societies" to the brutal syndicates we hear about in the news. Because of this, nearly every "Chinese Chamber of Commerce" group can trace their history to a Triad group, which means they can be anywhere that Chinese people live. Thing is, nowadays that's everywhere-- yes, there are still Chinatowns, but for the most part, Chinese people live in all sections of every major city.
What this means is, even if a runner team is less than discreet about having a safehouse or running a chopshop, they still have a good chance to escape notice. They can fake being associated with someone else, or simply not say anything and let everyone assume they're affiliated with another group.
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Please note that while I think that the mafia should knock on the door of whoever makes substantial money with a criminal business, I don't say that Shadowrunner should be paid little. I just say that if you want to play in a universe where runners are paid little, that's completely possible even if cars are expensive.
You lose... well, not "realism", given that this is a fantasy game; but you do strain suspension of disbelief. The era of Robin Hood Runners is long gone, runners are in it for the money. And if they can use their considerable skills and contacts to make more money doing other things, they would. For example, there was a long running problem where a mage could make so much money staying home producing orihalcum, they would never need to run again. My players actually asked me to ban it in my games, just to avoid the problem.
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For the payout, I think there are many different aspects to consider.
There are, and you just scratched the surface. Paying runners is very much an art form, and like all art, it depends on the results you want.
For example: I used to way overpay the runners. What this led to was that they started expecting more and more money each time, so the cash flow got bigger and bigger, until it was so bad they wanted 5000 each just to get out of bed and go to a meet. That's another thing you need to consider.
You also not only have to consider their goals, but which ones you want them to reach first, and what effect reaching them will have on the game. Wired 3 is expensive, but it's not really game-breaking-- powerful, yes, but not that bad, not even deltaware. So, I might want to contrive a way to give a player beta or delta Wired 3-- find a discount, have him do a favor for someone with connections at a delta clinic, that sport of thing. On the other hand, a really high Force Power Focus can break a game, even though it retails for less than delta Wired 3. So, I'd think of ways to slow down the acquisition of that. Same's true with really customized vehicles; in SR2, I designed a custom sports car that could shrug off missile fire, maneuver itself better than most live riggers, had enough firepower to level a city block, and could go slightly faster than Mach 1. It was dubbed the "Knight Industries Ten Thousand"

and I got it as a legal starting vehicle-- well under a million nuyen for everything, plus all my other toys. That was a much bigger problem than delta wired, even though the list price was a lot less.
You also need to consider story goals. For example, one character might be saving up a nest egg to retire. And that's a reasonable goal for a character, but it also means that if they get a big enough windfall, your campaign just ended. (Or, maybe you just lost a character.)
So yeah: there's a lot to consider, and it's all dependent on the table. There's no one right answer.
That said: I still advocate the high gear, low cash model. You do need to warn the players in advance, but that makes new gear into an entire adventure. You get better control over the cash flow, and you can better balance gear heavy characters vs the Awakened, because you can hand out the better toys as the magical characters advance. It worked well for me in many games, and I highly recommend it.