Also normal (non-government) NDAs let you sign away your right not to be punished for speaking about certain matters. I don't like it, but it's pretty well established.
Point is that—legally speaking—rights aren't actually inalienable.
Do you know the prominent cases of the examples you mentioned?
You can contract with another private entity to resolve disputes via arbitration, yes, but not with the state. The closest thing might be a plea agreement, but that happens after an indictment. You still have the right to a trial, but you may forego it if you choose.
I suppose if you're saying that a security clearance is like an NDA with the state, it's a reasonable comparison in function, but the means of prosecution is entirely different. It's like saying that everyone could be subject to UCMJ because of conscription.