Look at the appearance of the Hull, IMO Scott intended them to be a different ship-type.
The first Hull type is Pseudo Star Fleet while the new Hull type isn't.
Mind you, they could be the same species as the first aliens.
Plenty of SF writers have had Human "Good Guys" fighting against Human "Bad Guys".
They both use three warp nacelles with a ring connecting them all. Also, they both seem to use antimatter/matter for propulsion.