They are more art than science, providing an illusion of reality.
Nope, they are coded with the relation color = abundance of atomic component. Colors are a stimulus, they do not exist outside of all of our brains. What is real is the wavelength, and that, for instance, the transition of an electron from the 3rd to 2nd layer of the structure of the Hydrogen atom will emit a photon at 656nm, which we call red.
One disadvantage of the FITS format is that raw images typically need to be manipulated to show anything.
Nothing to do with the FITS format. That's the same type of information all RAW formats have : unprocessed data, as close as possible to the signal coming from the sensor after quantization, with ideally no processing, offset or other adjustments performed.
It made for great imagery, but wasn’t a true representation of how Jupiter looks.
Our vision is also subjective, it permanently adapt to lightning and ambient color conditions. There is no such thing as a true image representation. Especially in the mentioned case (a magazine), where it is desirable to have an image which pops the eye rather than a blob of washed out colors.
So what's the news here?