Re: The prefix number
Actually I think that's exactly why they existed. For situations where one Starfleet vessel would need to take control of another.
Kirk's line was "To prevent an enemy from doing what we're attempting."
That would men there was a danger, real or perceived, that someone could hack into a starship's command systems.
"A perfect organism, unclouded by remorse, or human illusions of morality." - Ash, Alien