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.
I think you hit the nail very close to the head on this.
Coming from the production side of things, it looks as if they were using a capping shutter in order to double-expose the forcefield outline over the first image.
The capping shutter allows for multiple exposures on a single frame of film before advancing the film to the next frame. The character cells and background would be exposed first and the shutter closed. The forcefield outline (colored outline against black) would then be placed over the cell and background, and the shutter would again be opened to expose this. That cell would then be removed and the film would be advanced to the next frame, with the same sequence repeated over and over until the shot was complete.
Now, as to the misalignment - it looks as if the lens was turned slightly out of focus for the forcefield exposure to make it softer. This would have the side effect of also changing the size of the forcefield image slightly - enlarging it so that it no longer precisely fit the background image - as evidenced by the outline shifting slightly and no longer fitting exactly over the smaller Spock image, and creating a slight inconsistency over the separation distance of the outline around Sulu's head.
Using this technique allows for every element to be on the original neg and keep the image quality high, and therefore save time and money on unnecessary opticals to achieve the same result.