The President is not the king of Law Enforcement
Despite the Republican claims when impeaching Clinton that he was the highest law enforcement officer in the land, that's not true.
As chief executive the President has considerable influence on federal law enforcement but he does not have operational control of all federal law enforcement.
The President cannot properly call the FBI and tell them to go search some guy's garage. That's not how it works. (Ask Nixon.)
The President is, however, the top of the chain of command of the armed forces. JFK could, and did, give a direct order to a low ranking Naval guy as he did during the Cuban Missile Crisis.
The fact that a policeman can shoot a terrorist who is trying to set off a bomb in Times Square (if alternatives don't work) does not necessarily mean that the US Military can do the same, with or without the President's order.
Some people do not care for a concept of unitary executive authority where the local police, FBI, IRS, NSA, etc. are all part of the Military chain of command.
This does not mean that the military can never do anything in the USA.
It means that some people prefer that some sort of public law govern such extraordinary actions.
And also, that if the military is to be another branch of domestic law enforcement then the military must be subject to Judicial review in the way Law Enforcement is... like getting warrants and such.
We cannot bootstrap military Independence from interference (okay because the military tends to operate overseas) into the same free hand for domestic law enforcement by saying the military is domestic law enforcement.
Yes, the military can act within the US in extraordinary circumstances.
It does not follow that the sort of secrecy and free hand we give the military means that the executive can act within America without accountability.