Actually the last mission we are talking about here has quite different problems from the ones you described in the main game. While varying difficulty is of course a problem it is on one side hard to avoid because of all the freedom a rpg grants, and on the other side kinda self regulated by that (leveling up elsewhere, better equipment, potions).
However this mission we are talking about here is played as dragon and with afaik predefined spells. You cannot do much before that point to make this easier. Now the second problem si that you are not responsible for yourself anymore because it is an escort mission.
This leads to a quite unrpg like situation where it is really all about some skill you have or do not have in this situation and that makes it quite hard for the people that do not have this particular skillset but rather a different one. This however in my mind makes it very hard for larian to change the mission in a way that does not make it ridiculous. I mean it is the fight against the invasion of damian, so even with the challange they put there, story wise I kinda thought... "If that's really all... why even bother with the main quest. As dragon I could have killed everything of that invasion force alone, all the time..."