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As far as I call tell, unless the spiritual electors wore their clerical vestaments, and they do not in those images, their elector's robes and those of the secular electors should have been the same color with only minor differences in the precise shade. I believe that the Golden Bull of 1356 specified the color of the elector's robes.
The other princes and nobles in the images are wearing their individual more or less normal and everyday costumes, and the colors of the individual costumes do not matter because a noble could wear pretty much whatever color combination he wanted to on any particular day.
The other thing where color matters is in the coats of arms. Any depiction of a particular coat of arms that is fathful to the verbal blazon or description of the coat of arms is valid, no matter how much different depictions vary from each other. Normally a heraldic artist should use the same batch of mixed paint to depict all the red in coats of arms in a picture like this. But if for some reason the artist had to mix up a different batch of red paint with a different shade of red to paint some of the coats of arms that would be all right, as long as all of the shades of red were clearly red and not any other color.
So long as the color is clearly red (gules), or clearly orange (tenne), or clearly green (vert), or clearly blue (azure), or clearly purple (purpure), or clearly black (sable), or clearly silver/white (argent) or clearly yellow/gold (or), the precise shade doesn't matter in heraldry.
The two versions of this image are depictions of the quarternion of the Holy Roman Empire, showing the Emperor, the seven electors, and four examples each of every rank of ruler in the Holy Roman Empire. So four rulers were selected from the rulers of each rank to be depicted with their coats of arms, or just the coats of arms would be depicted.
So there are lists of the coats of arms that are included in depictions of the quarternion of the Holy Roman Empire.
In the two images the arms are so small that it is sometimes hard to tell one color from another.
But even among the seven electors themselves, the upper image has an error in the coat of arms of the Duke Saxony, depicted as "barry agent and azure, a crown of rue vert", when it should be barry sable and or, a crown of rue vert".
Among the dukes, the coat of arms of the Duke of Lorraine was "Or, a bend gules, with 3 eaglets argent" but looks more like white with pale blue eagles in the upper image.
So if the colorists of the various different versions of this image couldn't always use the right colors or the same colors for the coats of arms, even though the colors of coats of arms are fixed by tradition and law, there is no reason to imagine they would try to color the costumes worn by the figures the same way each time.
The quarternion coats of arms were often depicted with each set of four on a different wing of the eagle in the imperial coat of arms.
Here is a link to an image and Aeliandil's answer lists the various coats of arms:
https://www.reddit.com/r/europe/comments/ekr1gi/the_quaternion_eagle_coat_of_arms_of_the_holy/1
Here is a link to another site which has several answers trying to list the various coats of arms.
I note that different states might be included in different versions of the quaternion, since it was an unofficial listing. This question asks why the Archduchy of Austria is not included in one version of the quarternion:
https://www.reddit.com/r/AskHistorians/comments/3cwc40/why_doesnt_the_quarter_eagle_contain_the_duchy_of/2
This Wikipedia article lists the coats of arms of many states in the Holy Roman Empire. But I suspect that it lists many that were not ever included in the quarternion and omits some that were in the quarternion.
https://en.wikipedia.org/wiki/Coats_of_arms_of_the_Holy_Roman_Empire3
Here is a link to the arms of the electors:
https://en.wikipedia.org/wiki/Coats_of_arms_of_the_Holy_Roman_Empire#Prince-electors4
The other coats of arms are not arranged by rank, as in the Quarternion, but by which Imperial Circle the states were members of. This makes it harder to compare the two groups of coats of arms.