What they mean by "change the damage calculations of tanks"?

[Alahra]

Dark Knight isn't vastly outclassed in terms of physical defense when compared to Paladin.

This is true. But your original question was:

How exactly is dark knight weaker in physical defense?

DRK doesn't have to be "vastly outclassed" to be weaker in physical defense. In fact, if it were vastly outclassed, there would be a pretty big balance issue. PLD arguably isn't vastly outclassed in magical defense, either, but no one would argue that DRK isn't better at magical defense.

And as a small aside, relating to Rage of Halone--even against a physically attacking mob in Azys Lla, the Halone debuff reduces physical damage by about 10%, so it'll reduce at least that much on the typical raid boss (and probably more since the boss should have a higher STR score).