Today, I had a number of things which required non-green highlights. I selected multiple lines, clicked ⌘-Shift-M to highlight as green, then clicked the pencil to select the color red — but only one line changed color. 
I then had to change each line one-by-one.
Perhaps something like the following — if multiple highlighted lines are selected:
- If you mouse-click the pencil to select a new color, all selected highlights change to that color
- Conversely, perhaps could type ⌘-Shift-M to cycle thru the colors. Ex:
- Select some text
- Type ⌘-Shift-M to highlight as green
- While text remains selected, type ⌘-Shift-M again
- Highlight color changes to red
- etc.