i don't think so. runes don't always scale to position in the game. for instance, the erdtree avatar in caelid drops 91k runes which is the highest amount of runes for any erdtree avatar in the game. are you "supposed" to go back to him while you're in mtop of the giants?

i think they drop a large amount of runes cause they're very hard and completely optional. if you want the challenge you can fight them, and you're rewarded with a prize that matches the difficulty. the last boss of the game is literally right after hoarah loux, 99% of the playerbase will beat hoarah loux and then immediately go to the next boss fight. it would be bad design if they intended players to fight malenia and mohg after loux.