defaults write com.houdah.HoudahSpot accentColor color_to_use
Replace color_to_use with one of red, green, blue, grey, or yellow (the default). Relaunch HoudahSpot, and you'll see your newly-chosen header colors. Hopefully a future release will bring a true pref with a color wheel to set the title bar background colors, but this is a usable workaround for now.
(This isn't much of a hint for those with HoudahSpot already installed, as they'll see the same message when they update the program. However, for those downloading the latest version for the first time, this hint may be of some assistance.)

