I don't think it's backlit; that technique was a little more advanced than what Filmation was working with in 1973-4 (though they did some pretty cutting-edge stuff with it starting with Flash Gordon
in '79). Note that the yellow aura around Spock isn't really any brighter than the white crags of ice behind him. That looks more like a simple double exposure to me, with the aura cels shot out of focus to create the fuzzy quality. So yeah, they would've been shot separately, explaining the misalignment. But it might've been an in-camera double exposure rather than something involving an optical printer.