In the event a boss became immune to magic damage you simply wouldn't enhance your weapon with magic. It really is that simple.

DRK has reprisal which like shield swipe is essentially a counter attack.

Before Swine if borrowed from is a magic counter and only would be seen in heavy magic damage raids. Kinda like how Dark Mind is mostly unused unless you know an attack is purely magical.

Sword spirit is debuff and ensures a crit(sounds a bit like a combo of SE/DE + Life Surge), Curtain would simply be an attack combined with a stoneskin/divine veil effect.

At least FF Explorers is true to form for all jobs. Dark Knight included.