I've noticed that oftentimes when I go to attack an enemy Fort, the scout combat report lists two separate threat levels.
What do each of these threat levels mean? Which one is the "real" estimation of difficulty?
There is a threat level for both the enemy hero located in the entrance of the town, and additionally the hero/armies fortified within the town. Right-clicked one will show the other in parenthesis (and vice versa).
By engaging in the siege you will fight two battles at the difficulties indicated. If, however, there is no garrison hero, the garrison and the visiting hero will combine forces, and you will only fight a single battle.