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

[Alahra]

How exactly is dark knight weaker in physical defense?

Shadowskin and Shadow Wall are 10% weaker than their PLD counterparts, Rampart and Sentinel, and PLD also has the ability to block physical hits via shield. In practice the difference is not enough to prevent DRK from tanking physical hits, but it is in fact weaker in that department when compared to PLD.