Ballista and towers.

maybe the primary skills of the heroes who are fighting are taken into account here???

Right here, I think—this plays a significant role, if we are comparing them to the primary skills of the garrison, whether it's the hero or monsters.

after all, some have more defense, which is why the damage is lower... and vice versa

Now here—I disagree... You know what the "Air Shield" spell does, right? Only when it's used do towers somehow deal more damage to the creature it was cast on! Why, it's hard to say.
Yes, and in my opinion, this isn't the only spell that "increases" a monster's defense, say by 2, while tower damage increases by 10% (don't judge the numbers—look at the meaning :))