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Deke Slayton, who was the Chief Astronaut had originally planned to be inside the capsule for the communications test. He would have had a tight squeeze as there was only room and couches for 3 people (I believe he had intended to lay on the floor). Before the test he decided that his presence in the capsule would present too many poblems and changed his mind.
So there were not 4 astronauts on Apollo 1, but there nearly was.
He'd have stowed himself down on the floor of the lower equipment bay, "beneath" the feet of the astronauts in their couches. There was room for someone else in there.
As to a "secret astronaut program", there was no such thing. The only astronaut program we had was the one everyone knew about.