The rules that you've quoted are pretty clear. You gain advantage when attacking unconscious creatures, and you gain disadvantage when attacking prone creatures from further than 5 feet away. If you have both advantage and disadvantage — you're attacking an unconscious creature from further than 5 feet away — you get neither, instead.
The halfling's Lucky trait deals with the die roll (PHB, p. 28):
When you roll a 1 on an attack roll, ability check, or saving throw, you can reroll the die and must use the new roll.
And so does Advantage/Disadvantage, since it refers to the same trait (PHB, p. 173):
For example, if a halfling has advantage on an ability check and rolls a 1 and a 13, the halfling could use the Lucky trait to reroll the 1.
The Divination wizard's Portent feature, on the other hand, deals with the check as a whole:
You can replace any attack roll, saving throw, or ability check ... with one of these foretelling rolls.
And here comes the interesting part - the three emphasized terms are only mentioned in rules as actions, not numbers:
The description of attack rolls (PHB, p. 194):
To make an attack roll, roll a d20 and add the appropriate modifiers.
If the total of the roll plus modifiers equals or exceeds the
target’s Armor Class (AC), the attack hits.
Saving throws (PHB, p. 179):
To make a saving throw, roll a d20 and add the appropriate ability
modifier. [...]
A saving throw can be modified by a situational bonus or penalty [...]
[...] proficiency in a saving throw lets a character add his or her
proficiency bonus to saving throws made using a particular ability
score. [...]
And ability checks (PHB, p. 171):
To make an ability check, roll a d20 and add the relevant ability
modifier. As with other d20 rolls, apply bonuses and penalties, and
compare the total to the DC.
All three go the standard way:
- Roll a d20, get a number
- In case of (dis-)advantage: roll another d20, get a new number (or
keep the old)
- Add bonuses/penalties, get the final number
- Compare the final number with the AC/DC and get the final
success/failure answer
From the strict RAW reading of Portent, we have to replace steps 1–4 (the whole check) with a number (foretelling roll), which makes no sense, as the result has to be boolean – success/failure.
If we loosen the restrictions, the logical thing to say would be "In the context of Portent, attack roll/saving throw/ability check is the number to be compared with the AC/DC" (i.e. the result of Step 3 above). In this interpretation "You must choose to do so before the roll" means that the decision is made before Step 1 and therefore no actual die roll happens. The modifiers are applied to the foretold roll as normal. This interpretation is reinforced by an unofficial tweet from March 2015 by rules designer Jeremy Crawford:
The portent die is intended to replace a d20 roll only, not any modifiers applied to it.
This result is Rules As Intended as well; the whole point is that the character knows in advance what is going to happen.
Best Answer
The attacking enemy has disadvantage on the roll.
The relevant quote from the PHB is here:
It's pretty clear that, in order for the advantage and disadvantage to cancel out, the roll has to have both advantage and disadvantage. To use computing terms, it's an exclusive OR gate. A roll can have advantage or disadvantage, but if it has both, it gets neither.
The Elusive class feature could have been worded in a number of different ways, but the way it is worded makes it clear that a roll can never have advantage against a non-incapacitated Rogue 18. The only way that a roll can have advantage and disadvantage cancel out is if it has both at the same time. Since a roll can never have advantage, it can't have both, and instead keeps the disadvantage.