"Rule of One - The most important thing to do is stick to one ship, energy weapon type, and projectile weapon type."
Thats pre-Season 5 information actually, before they changed the Skill tree.
You can use whatever ship you want now with no downsides.
Energy weapon type, yes it is important to run ONE energy weapon type with the corresponding consoles.
Torpedos are also important to use the correct console type with the torpedo you choose.
The point of that rule was that you had to put SKILL POINTS into those specific ships/energy weapons/torpedos, which if you did not use those ones you put skill points into your damage was handicapped badly. Thats not the case anymore, its more dependent on the consoles now.