Hypo #2: The Pres gives the order to take into custody in any manner a political opponent, with the reason being National Security. So secure even the reason(s) can't be disclose. We establish that the order goes up to a high officer who talked to the President just before giving the order. The opponent ends up comatose in the hospital.

Again, though, if you actually look at what this involves it's hard to see how there could possibly be both a crime and immunity.

Suppose the President "gives the order" to take someone into custody. The immediate next question is, "How can we get a warrant for their arrest?" Because under the U.S. Constitution, if the government is going to take someone into custody, they have to obtain a warrant to do so. And they can't get a warrant without probable cause. There are loads of specific exceptions (officer witnesses a felony, traffic stops, Terry stops, etc.) - but there isn't a generalized "National Security" exception. The Executive's authority to take into custody someone on U.S. soil is bound by the 4th Amendment.

So, assume the above hypothetical. The President has given the order to take a political opponent into custody.

If that order is given (and followed) through normal channels, then the FBI (or whomever, but it would probably be the FBI) will have obtained a warrant for the arrest - and will thus have needed to disclose sufficient reasons/evidence to the court to establish probable cause. If that's the case, then what crime has the President committed? Because the warrant was issued, we know that the President didn't just make up the National Security reason out of whole cloth, and the determination that the person should be detained was reviewed by the judiciary. It's hard to see how that's the basis for any criminal proceeding against the President.

What if the President orders the FBI to not obtain the warrant and just go ahead with the seizure without it? Then he's clearly engaged in an act that's not only outside his authority, but which he is directly prohibited from doing by the Constitution. He can't then claim immunity for that act, under the majority's reasoning.