When Color Coding by Velocity is enabled, MIDI notes are all the same red color (hue) on all tracks displayed, and MIDI notes vary in color saturation (from a light red to a dark red) based on the Note On velocity. Notes with low velocities are lighter in color and those with high velocities are darker.
When neither Color Coding by Track nor Color Coding by Velocity are enabled, notes are drawn in the MIDI Editor in as the same color they are in the Edit window—using the color coding options as set in the Track Color Coding settings in the Display Preferences.