Questions could worded a bit better, but you’re basically asking for damage vs defense formula. This is the closest I’ve found on this.
So in your first example. 500 atk vs 500 defense, each tile would do 1 to 33 dmg assuming no crit effect. If you apply %atk buff and -def debuff, the damage will shoot up in a nonlinear fashion according to the graph. This is why buff and debuffs are so good.
How the %atk from special gets applied against defense I’ve no definite answer. My suspicion is that defense mitigation gets applied to the base atk before %atk from hero special is applied to scale up the resulting damage. This is why Thorne is such a trash attacker and hits like Sonya… because his base attack IS Sonya’s atk stats.