Hi delph,
Here is my interpretation. Portent replaces the attack roll / saving throw. This means that your portent dice becomes the result of the entire roll, not just one dice. So, if a creature has advantage / disadvantage it does not matter. He does not get to roll dice at all, just uses your result.
On the other hand, Indomitable allows you to re-roll a result. Therefore, if you use portent on his first roll, that's the result. The enemy could then use indomitable to re-roll that result.
Similarly, a character could use the lucky feat to roll an additional d20 when you use portent and take the result of their choice.