No need to change the availabilities. Afterall, without ammo, a gun is just a fancy club. Make it hard to get ammo outside of legitimate, SIN-tracking methods, and even if the gun is easy enough to get hold of, you won't find people going crazy with the trigger against you. Meanwhile, if you make the ammo, you can always toss in a few clips as part of the deal when working with runners.
But high power ammo isn't "hard to get ammo outside of legitimate, SIN-tracking methods", it's totally illegal to own, thats massively different think.
And gun that can only fire such ammo, shouldn't be something you can get with a licence, as that doesn't make any sense. Who the heck would sell(and who the heck would hand out licences for) guns that can't be legally used at all.
Why is it different? If it is totally illegal for civilians to own, then would it not be hard to get outside of sources with corporate or military connections? Restricting the flow of ammo, especially for weapons that only take that kind of ammo, means that you can equip people with guns when they work for you, but it is harder for those guns to be used against you in the future, since you are the one who makes the ammo. Meaning that the weapons themselves are less likely to 'fall off the back of a truck' than ones that can take more types of ammo, so these higher end weapons are going to be relatively rare when you're facing off against 'terrorist groups' (read: Shadowrunners, organized crime, and the like). It is a subtle means of control to keep people in line with your interests, much like how transport fees on, say, food that go up and down with the 'instability' of an area may persuade locals to toe the line.
Okay here we go, ammo, high powered or "Milspec" or not, isn't that hard to come across. The ammo shouldn't be F, unless it has no purpose other than military application, like explosive ammo or tungsten flechettes. High powered ammo should just be a modifier to ammo that increases its price by a bit and its availability by +2 or +4. It's not the legal issues I'm trying to point out so much as how stupidly common bullets are, home defense magnum JHP ammo or just regular bullets, some are going to be harder to come across and be marketed towards law enforcement but bullets are cheap and ubiquitous.
Bullets may be, Aryeonos, especially in the real world. However, we're talking about a game world, where there are controls in place to keep people from doing stupid things like modding an assault cannon to FA and making it belt-fed. As for why the ammunition is controlled, read above. Perfectly legit, in-game reason for ammo to be restricted more heavily than weapons. It is another level of the corps trying to control the criminal element. If you accept that criminals are going to get guns, regardless, then by making certain types of ammunition more difficult to obtain, you can coerce people into getting less threatening ammo for their weapons, or force them to be more particular with how they use their ammo. It isn't about the ammo itself, but about trying to control behavior.