They wouldn’t. T2 spec skills only apply to T2 mods. In this case, T2 mods get a ROF bonus. Faction mods may be able to fire T2 ammo, but they do not get the T2 spec skill bonus to ROF.
Just tested in Pyfa, and it seems even if you have Spec 1-2, you’ll end up doing more damage than the Factions. Which is lame, b/c I know some of the other guns under-perform until you get Spec 4-5. Then the T2 mods finally pull ahead.