That assumes Dominator uses (Dual) Flak for mediums. If medium mounts get artillery like Maulers, it can focus fire a lot of artillery at targets. Ever since Vulcan cannon was buffed, it is sufficient for most PD, and great as a finisher when it is safe to approach. Yes, dual flak is better PD, but I rarely get to situations where dual flak can defend against things that Vulcans and shield could not. Also, if medium mounts get assault (or so-called "fire support") weapons, then missiles need not always be Annihilators.
For max DPS, I suppose a Dominator can use heavy ballistics, Maulers, and three light needlers upfront, but that hurts frontal PD.
Dominator's main weakness is sub-par agility and top speed (without Burn Drive) and much of its firepower can only be directed forward.
As for AI, it uses my favorite configuration fairly well, which is Mjolnirs, Maulers, Vulcans, and Pilums.