Where to start with the inaccuracies in this paragraph?
First, the judge implies the Supremes reversed Lincoln's position during the war. This is inaccurate. The case he is referring to wasn't decided till 1866.
Second, the Court nowhere says that the government must give such protections to all people everywhere. It said military courts could not be used to try civilians in those areas where the civilian courts were functioning. Obviously, military courts would continue to function for military personnel, including enemy combatants, everywhere. And military courts could continue to be used to try civilians in areas where civilian courts were not functioning. IOW, in combat zones. Or, as in the South during the war, in areas where the US courts were not functioning due to insurrection and rebellion.
Finally, the Court has never said " the Constitution guarantees its protections to everyone that the government restrains, no matter the crime, no matter the charge, no matter the evidence, no matter the danger." If it did, legal enemy POWs would have full constitutional rights, and they just don't.
And by any reasonable definition, illegal enemy combatants should have fewer rights than honorable legal POWs.
I have read the text of the Act in question. It specifically says it doesn't apply to US citizens anywhere in the world, or to legal residents within the USA.
Not exactly. It describes HOW the law will apply. That military detention is not required when the detainee is a US citizen.
Does the NDAA Authorize Detention of US Citizens? - Lawfare (Robert Chesney) December 1, 2011
Section 1032 is the supposedly-mandatory military detention provision--i.e., the idea that a subset of detainable persons ("covered persons" in the lingo of the statute) are not just detainable in theory, but affirmatively must be subject to military detention (though only until one of several disposition options, including civilian custody for criminal trial, is selected). Section 1032 then goes on, in subpart (b), to state expressly that US citizens are exempt from this "mandatory detention" requirement (though lawful permanent residents are not).This obviously rules out the idea of a mandatory military detention for US citizens. But note that it tends to rule in the idea that the baseline grant of detention authority in 1031 does in fact extend to citizens. Otherwise there would be no need for an exclusion for citizens in section 1032, since the 1032 category is a subset of the larger 1031 category.