The enemy you are hitting may have different armor and resistance values, which would mess with calculations a bit. Armor being the defence vs physical and resistance defence vs special.
In general, special damage is higher, but with a lower base crit chance, and character resistance is lower than armor. So usually special damage will be better but it's balanced by easier crits for physical. Damage output is really dependent on the offence modifiers for each ability, which are not presented in game. You can look them up on swgoh.gg, but it won't show you both the old and new.
