I agree and disagree with this.
I think the carrier skills should only apply to combat ships in the way Tactical Drills and Crew Training are already configured.
This way, you're not diluting your carrier skills by giving them to non-combatants. You could have the carrier skills apply to them by installing Militarized Subsystems, which you would already be doing for the boost from Crew Training and/or Tactical Drills. (If you're in Leadership, you probably got Crew Training.)
As it is, Tempest really does benefit from the carrier replacement rate skill (as do a lot of mod ships), and I wouldn't want it to lose this bonus. The buff to Tempest seems neat, but part of the reason for the Termination Sequence system was to make the Tempest less consistent while still having damage spikes, right?