Understood but, IMHO, not really relevant here. One, Congress has not declared war. Two, the commander-in-chief clause generally does not grant domestic law enforcement powers to the federal executive short of scenarios involving civil war, invasion, or insurrection; domestic law enforcement, constitutionally speaking, is a state matter.
Bottom line: wage war without quarter on terrorists abroad, by definition they are ineligible for Geneva Conventions protection. Domestically, however, different rules apply. If the authorities have probable cause that a crime has been committed or suspect a conspiracy is afoot, they can obtain a warrant per Amendment IV. Claiming constitutional authority to declare anyone, even American citizens on American soil, as enemy combatants subject to indefinite detention without trial, as the current administration has done, is risible.
Moreover, the government can always secure the border and largely prevent the entry of enemy combatants to begin with. Government claims that we are at “war” would have more credibility if officials seriously addressed the border issue - securing the perimeter is also sound military practice.
I think you are confusing the President's war making powers under Article 2 with the President's law enforcement powers. Listening in on enemy communications has nothing to do with law enforcement. Signals intelligence is what we did when we broke the Japanese code and learned of their plans to invade Midway Island in World War II.
Think of it this way, if FDR was listening in on conversations between the German High Command and Nazi spies in the U.S., would he have had to have a warrant first? Of course not. The warrant requirement under the Fourth Amendment only applies to unreasonable searches and seizures, which has been interpreted to mean searches and seizures conducted as part of law enforcement. The courts have never considered Signals Intelligence to be an unreasonable search and seizure.