If the premise is that misalignment must be explained by cels being shot separately, then how does one explain misalignments such as those of the elevator doors in the shot of Cyrano Jones standing on the bridge?
Just because that's one
way images can be misaligned, that doesn't mean it's the only
way. See what I said above about registration errors. That would be the reason for a misalignment most of the time in cel animation. Double exposures are a separate technique that would have their own distinct causes for a misalignment. In the former case, the misalignment would result from haste -- in going through the mechanical motions of switching out one cel for the next for the next and photographing them one at a time, a hurried animator might not notice if a cel is misaligned. In the latter case, the animators can't actually see the images together until the film is printed, so they'd be estimating their placement by measurement, and differences in focus or film printing might throw off the relative sizes of the two images, creating a misalignment as seen in the "Slaver Weapon" screencap above.
Couldn't they have just airbrushed paint on cels to make the belt auras and shot them in one exposure with the rest of the elements, the way I assume they shot most every other frame?
They probably did that on some occasions. But the blur on the auras around Spock and Sulu in the screencap above looks like an out-of-focus image, not an airbrushed line. Look how much fainter the Spock aura is -- it's a thinner line, so the width of the blur overwhelms it more than the thicker line around Sulu.
And if it had been airbrushed in a single exposure, it wouldn't explain the misalignment in that screencap. Note how the position errors get bigger the farther you get from the center of the image, as if the "aura" artwork was zoomed in more.
Although I suppose it's possible that it could be a cel that was positioned a bit closer to the camera rather than resting right on top of the others, so that it would be slightly out of focus. That would also explain the positioning issue. But it does look like a double exposure to me.