That would be the minister of defense. Pinochet was in charge of the army, not the country's armed forces as a whole.
Yeah. There was no Allende.
There was also no constitution, de facto or de jure thanks to Pinochet. Frei could at least appeal to the constitution in his campaign against Allendism. The Pinochet junta precluded that possibility.
The defense ministry was vacated with the arrest of its criminal occupant the morning before the coup. The four branches of the military put Pinochet in charge of the whole armed forces that morning because his branch was the most senior.
There was also no constitution, de facto or de jure thanks to Pinochet.
Actually you can thank Allende for that. The constitution was recognized to be in a state of dysfunction at least three weeks prior when the Chamber of Deputies met and found it usurped by Allende. That is why Frei specifically described Pinochet's action as legal.