The School of Divination wizard's Portent feature states (PHB, p. 116; emphasis mine):
You can replace any attack roll, saving throw, or ability check made by you or a creature that you can see with one of these foretelling rolls. You must choose to do so before the roll, and you can replace a roll in this way only once per turn.
In the introduction to the PHB (p. 7) and basic rules, the 3rd paragraph under "The D20" describes saving throws, attack rolls, and ability checks as (emphasis mine):
[…] the three main kinds of d20 rolls, forming the core of the rules of the game.
All three of them consist of a d20 roll and then modifiers are applied to this die roll.
The description of Portent is quite foggy. The first sentence suggests that it allows to replace the final result (d20 + modifiers); however, the second part of the description mentions the roll, without specifying if it just refers to the d20 roll or to d20 + modifiers.
Does the Portent feature allow the Divination wizard to replace just the d20 roll? Or does it replace the final result?
This topic is covered in several answers and questions related to Portent working with other rules/aspects of the game, but I believe that this aspect of Portent needs a dedicated question. Some of these answers cite tweets by rules designer Jeremy Crawford. On one hand, the Sage Advice Compendium ("Official Ruling" section) states that tweets are not considered official anymore; on the other hand, in the very same section it also states that Crawford's tweets could be a preview of rulings that will appear in the SAC. Crawford's tweets about this issue here and here have not been still included in any version of the Sage Advice Compendium, to the best of my knowledge.
Best Answer
Portent makes you replace only the d20 roll, not the final outcome.
The description of ability checks in the rules says (PHB, p. 174):
The descriptions of saving throws and attack rolls have the same phrasing.
The description of the Divination wizard's Portent feature says that (PHB, p. 116; emphasis mine):
It does not say to replace the whole d20 + modifiers. Hence, the Portent feature allows the Divination wizard to replace just a roll of the d20, and not the final outcome, following the wording of the feature.
Replacing the final outcome (and not just the d20 roll) would allow the wizard to force the possible outcomes to lie in the interval \$\{1,2,\dots,20\}\$ and not in the interval \$\{1+x,2+x,\dots,20+x\}\$, where \$x\$ is the eventual modifier. In this way, a modifier would play no role in an attack roll, ability check or saving throw. Indeed, forcing the final outcome to lie in \$\{1,2,\dots,20\}\$ is equivalent to having all the creatures with a 10 or 11 score in each ability (hence \$+0\$ modifier) and without any circumstantial bonus (e.g., proficiency bonus, a racial bonus, or some combat feat). For example, in this way a CON saving throw of Hobgoblins and Ancient Red Dragons would range between 1 and 20 for both creatures, while normally it would range in \$\{2,\dots,21\}\$ and in \$\{17,\dots,36\}\$, respectively.
This answer is supported by other ones related to Portent working with other game elements (such as Rubiksmoose's answer to a question about its interaction with Bardic Inspiration, and my answer to a question about its interaction with advantage/disadvantage). Here I consider another aspect that supports my ruling: if Portent allowed to replace the final outcome, then it would mean that all the creatures have no differences at all, from the point of view both of abilities scores and other characteristics such CR, feats and similar.