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The government can exempt themselves from IP laws. For example, the government has exempted itself and defence contractors for violating patents (to build top secret devices) in the past.

Yeah, not going to happen because of "the national security interest of the United States". A related concept is a contract contrary to public policy.

Alas! Sovereign immunity means you can't sue the government without their permission.

Where are you going to sue the government... in a government court?

...yes? Couldn't there be valid causes of action for government acts? Are we simply assuming bad faith on the part of the government for any possible scenarios?

Only in a revolution, I suspect. And revolutions are not to be undertaken lightly.