I completely agree with your point, but not your conclusion. As someone who is now regularly using all the custom colors I would have to go in a manually choose one additional color…
Separating the functions adds only one more step for users (such as myself) to go in and color coordinate (not to mention that this step already exists for every other color, just not green). BUT this also restores a separate function highlighting.
For users who only highlight (which is not me), they now have the option to highlight with the color that bests matches their chosen theme (and retain the vibrancy). They are no longer restricted to a green that doesn’t match their theme.
For users (such as myself) that do both (highlight & color coordinate). I am now able to distinguish and separate two different greens (for example). Now, I can color coordinate, with a color palette that matches across different colors and themes. I am also able to have a separate color, that does standout and does not match the other color pallets- allowing me to quickly visualize the difference (i.e., a highlight).
I understand the cost is adding one more step for green, but the return is having another function that does act separately (i.e., highlighting vs. color coordinating).
I wouldn’t be opposed if there was a separate syntax for color coronating (i.e., not the ==syntaxt==, which is also being used for highlighting). But i think that would just be outside the limitations of markdown and instead i have just developed a keyboard shortcut to quickly choose different colors…