^^^
AND... all custom themes (Tungsten & 3rd party) are stored and accessed outside of Sonar's operational files so it can't manipulate them in the same manner it does Mercury.
It's also possible (tho highly speculative on my part) that custom themes overlap the Mercury theme, covering it up, making it more difficult for Sonar to manipulate them.
Even so, it has been mentioned in the past that colorization of custom theme tracks may be possible in the future.