I'm fine with encounters getting more challenging. I'm not fine with having the SAME CREATURES scaled up and down. Consistency is an important part of what makes a setting somewhat believable.
Agreed. Adding creatures but keeping them fundamentally statistically consistent is IMO the best way to scale difficulty. Or change them to higher caliber troops/enemies that are internally consistent in the hierarchy of foes.
Bonus point if it's built into the narrative
why too (ideally nothing too overt, but subtlely hinted). I.e. if you attacked Base A, Base B of the same faction gets more difficult because they are now expecting you. Or doing quest Y first makes quest X harder because the X now had time to gather reinforcements.