Over 4 years ago I did some calculations and figured out that 2nd form monsters take 74% of the damage compared to a final form. I assume they put this into the damage calculation at the beginning of the game to account for monsters not having fully trained stats, because otherwise they would die incredibly easily.
Bear in mind that the actual defence stat of monsters (the number itself) does not matter. What matters is the relationship in stats between attack and defence. In the case of Aurodragon(s) and Shadowyrm, they are both “full attack” stats so they will take the same amount of damage from attacks. The only factors that I’m aware of that would make them take different damage are the ±10% damage variance and the lower form defence buff (which I calculated as a 0.74 multiplier to the damage dealt all those years ago). That roughly lines up with your example of the damage dealt.