The skill points from a class mod act the same as the real deal. If you have a class mod with a skill bonus for something you don't have, it won't apply. The points from the mod that exceed five, such as a spark level of three through five will still benefit from the extension. Each skill has a set bonus per level, and the more levels the more cumulative bonuses. A class mod bringing a skill total above five will add the bonus that many times. I.E. Phoenix skill modded to 9 would present an overall bonus of nine fire, and a 45% ammo save chance.