I'm a little unsure about what you're asking.. for simplicity, let's take the Kol's Guass Blast ability. It fires one projectile, and does I think 300/550/800 or whatever damage.
You're asking if modifying the number of projectiles through burstcount will modify the damage for the ability?
If that's the case, then no it won't.

The Kol's ability, for example, has the weapon effect in its ability file, AbilityGaussBlast, which calls BuffGaussBlast to apply the actual damage (through buffActionType "DoDamage").
This makes the "buff" application separate from whatever effects you attach to the ability.
Did I understand your concern correctly, and if yes does that help?