So if I can steal your money, it's not rightfully yours because I am only permitting you to have it if I don't steal it? The government didn't grant rights. The rights are assumed "self evident". Even voting rights are assumed to be corrections to injustices, not charitable relinquishing of rights. What person has the ability to issue rights? All they can do is honor them, but even if they don't, it doesn't mean the rights don't exist. Only you can relinquish your rights, and that's what the caveats propose you do in certain situations. You aren't required to be in a crowded theater, nor are you required to be in a place where more than half of their income is derived by sale of liquor for consumption on premises. Those are some of your options, but to make those options you know that you give up your legal permission to carry a firearm, or to yell "fire" in a crowded theater and incite panic. If a court of law found you were within your cons utional right to do these things even if it was against the law, the law would have to be changed. The 5th Amendment is about self incrimination. The 4th is about unlawful search and seizure.
The 2nd Amendment says "shall not be infringed upon". Becoming a prisoner has always caused you to give up your ability to exercise your rights. Joining the military does something very similar. In those cases you aren't giving up your rights nor are they taken from you. You still have the rights, you just cannot exercise them. Permission has always been the roadblock to rights, but that doesn't mean rights don't exist. You wouldn't say people don't have basic human rights simply because they aren't being afforded the decency of them by some dictatorship like PRNK.
The purpose of the BoR is to tell government what they cannot do, not to tell people what they can do. The rights list isn't exhaustive.