Larian, being the game designers, are taking the part of the tabletop GM.
Traditionally, and written into every rules edition of D&D that I remember, the GM has the right (the duty, even) to alter the existing rules to suit the group's preferred gameplay style. As CrestOfAstorias says, height does not automatically confer any bonus or penalty, but this is where a tabletop GM would step in and choose to give Advantage or Disadvantage.
So, the rules as written are not the same as the situation in the game, because the 'GM' (Larian) has declared it so. As with any other such ruling, I dare say that it will be assessed and reassessed, and either toned down or kept as it is.
I agree that Larian are the DM implementing their own house rules, but at some liminal point when you change lots of rules, it stops being D&D and becomes something else entirely for better or worse. I don't claim to know exactly where that line is drawn, but Larian have crossed it.
