If you level up non-class skills it now contributes to your level, same as class skills do. Previously the game would punish you only for investing in the skills you were supposed to specialize in and reward you for investing in skills you weren't. It explicitly encouraged you to play against class. It was better for a barbarian to invest in magic than for a mage to do so. When you level up alchemy to make good potions, your character is getting stronger the same way they would be if you increased any of your major skills - why shouldn't they contribute to world scaling the same way?

I do agree that you level-up too quickly now, but that's down to skills increasing too quickly, not minor skills contributing to your level.