Controversially, courts have upheld that citizens can sign away their right to a trial by jury; it's called binding arbitration.
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.
If constitutional rights can be signed away with the stroke of a pen since they are alienable... then a lot of absurdities become possible, such as someone selling themselves into slavery and so on.
Do you know the prominent cases of the examples you mentioned?
> citizens can sign away their right to a trial by jury; it's called binding arbitration
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.
Isn't that the same than a doctor signing away his right to divulgate his parent information (or a lawyer), or even more mundane, for a tech guy to publish the source code of his company ? (it's an actual question)