It’s just based on its own separate damage value. In the case of Helios, yes, a fire damage boost would boost it. Unfortunately, due to the fact that these skills are based off of their own value, they become weaker and weaker as the game goes on, paling in comparison to the power that a gun can do due to the fact Rank-Damage based skills level-scale in weaker amounts.
So to use those skills, you either gotta really like them anyway, put some work into specifically making them shine, or just like how they LOOK or something. Maya’s ‘Cloud Kill’ is a good example. Great skill early on, CHEWS through armor enemies. But by the time you hit even Level 50, it takes longer and longer to do significant damage with it. Cloud Kill has become widely known as the worst skill in the game and actually detrimental to the player. A lot of Maya’s skills suffer from this… actually. Very, very unfortunately.
This isn’t to say NOT to use those skills though. Some of them can have niche uses, or surprisingly good effects in SOME situations. Blight Phoenix for example. While it doesn’t do much damage by itself, it WILL keep Melee attackers away from you when it activates. So experimentation (and sometimes stubborness) might be what you need to make weak skills alright.