If the zombie has resistance or vulnerability to the attack, the DC is calculated by the final damage amount.
From PhB: Resistance and Vulnerability
For example, a creature has resistance to bludgeoning damage and is hit by an attack that deals 25 bludgeoning damage. The creature is also within a magical aura that reduces all damage by 5. The 25 damage is first reduced by 5 and then halved, so the creature takes 10 damage.
The amount of damage the zombie takes (which is the input value to Undead Fortitude) is the result of the final damage calculation, after all modifiers.
However, the DC is independent of the zombie's remaining HP
From the question:
Do I set the DC to 5 + the damage that was rolled against it, or do I set it to 5 + the health it had before dropping to 0? I've not found any rulings on the matter.
Creatures can take damage beyond their current hit points - but the result of that damage is normally to set their HP to zero.
From PhB: Massive Damage
For example, a cleric with a maximum of 12 hit points currently has 6 hit points. If she takes 18 damage from an attack...
If damage taken was capped at current hit points, it would not be possible for the cleric to take 18 damage from an attack in that example. Similarly, the damage a zombie takes is not capped at its current hit points either. If it takes 15 damage from an attack, the save DC is 20 regardless of whether it had 15 HP or 1 HP before.