To my mind, difficulty should be determined by win/loss percentage of a quest with the available cards. For example a scenario that you win 50% of the time you play it should be difficulty 5 and a scenario you win 70% of the time you play it should be a level 3. This is why I keep a reccord on Google Docs of my wins and losses each time I play, for each scenario. This lets me look back and compare my win ratio to the difficulty level to see how close FFG got.
For instance, 'Into the Pit' and 'Watcher in the Water' both match up exactly with the difficulty level assigned to them. In contrast, Dead Marshes is way off because I've never lost a game of it out of 10 plus plays even though it's Level 5. Of course FF probably doesn't have the time to play a scenario as many times as it would take to get a clear picture every time.
Difficulty level is based on encounter sets which is create encounter deck. Look for example to second cycle: every quest which is content encounter set (i dont remember the name) with a Moria trolls, Orc Drummer and Drums in the deep is always difficult 7 or higher (in the case of Shadow and Flame is 8).
So actually in theory you can change encounter deck in any quest to make it more interesting and difficult.