Customizing companion energy colors appears to result in the companion's default energy being overwritten, defaulting to another color entirely, often a shade of gray/white. As I have seen no evidence to the contrary, I would assume this behavior is unintended. Moreover, this occurs regardless of method used to change the default color to a custom color, i.e. manually picking a color versus using the randomize option.
Below is an example of the bug, in which the default emissive color has also been overwritten. This is most visible in Vulphaphylas, Predasites, and Helminth Chargers.
