It's boosting the defense not associated with the monk's secondary stat. The Stonefist monk has high STR, and thus decent Fort already.
While I can agree with the concept, they should not have called it "Mental Equilibrium". That screams +1 will to me.
Instead call it "Mind over Body" or something similar, and then it makes perfect sense.

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.