This sounds like a confusion of separate incidents in science. Einstein did not use relativity to predict Pluto. He used relativity to predict the bending of starlight near the Sun. What happened in 1919 were observations of a solar eclipse by Sir Arthur Eddington which confirmed the shifting of apparent position of stars near the sun (which could only be observed during such an eclipse).
Pluto's existence was indeed foretold by certain perturbations in the orbit of Neptune. (Not by Einstein, IIRC, however.) It and its moon Charon were eventually found about where the predicted object should have been. There's a hitch, though. The Pluto-Charon system isn't massive enough to have caused the perturbations used to predict it in the first place. Either those observations were spurious or there was something else out there.
It was Lowell who predicted Pluto in 1915, but finding it fairly close to his predicted position was actually pure luck, because it isn't what causes Neptune's orbital perturbation (I think it isn't large enough); there is something else out there, as yet undiscovered.
Einstein's successful prediction was of the precession of the perihelion of Mercury's orbit, due to the distortion of space by the sun's gravitional field.
It think the author is confusing the prediction of the precession of Mercury's perihelion with some sort of test of SR. He's got it all mixed up. You're right about the bending of starlight being the falsification test of GR.
It's too bad; the author's analysis of Popper and his conclusions re: ID are spot on. Oh, well, that's what one gets when one lets a philosophy nerd write an article.