Not all pan and scan movies were created equal though, especially movies made after pan and scan became a thing as many movies were shot with pan and scan in mind. That leaves us with some movies that were actually cropped for cinemas and even more common movies were neither version can ever be a definitive version as there will always be missing footage.
The X-Files is the only example I can easily google so yeah a matter of preference in this case if you prefer more "side" information or more "upper/lower" information. In some movies the choice is easy, in others it depends on the scene.
I'm not saying TMNT 1990 is like this but I know its true for Jurassic Park where the VHS actually has extra information that the "superior" widescreen format doesn't have.