The color by track / media item functionality is newer than midi_note_colormap. It doesn't use it. Ah! you're thinking, then it probably calculates the difference between the MIDI editor note selected and unselected definitions, right? Nope.
Reaper appears to lighten the note colour and give it a white outline. IIRC, its just one of those many, many things in Reaper that are not themable.
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