Oh you got a point there.
There could be a potion that increases fire damage or something.
There are potions that directly increase the damage of all destruction magic.
Either that or the game does calculate for higher ranks of perks, and his are bugged somehow. This seems most likely, because the +damage perks do not work on fire rune or flame cloak, which is the case here. I think potions do affect them though, but I'm not sure.
Also these multipliers are bizzard. Flames does about 3.5x base damage, while firebolt does about 2x. Bizzare.