You can always run a test.
1. Select a theme and change all colors to green in TE
2. Take screen shots of every view
3. Change all colors to yellow in Preferences
4. Take screen shots of every view
5. Compare screenshots
P.S. You may need a whole weekend to do this.
But seriously I would think that you can set a color in the TE and then override it in Preferences if they affect the same item.
Then if you set a Preference color and afterward change to a new theme it might override that color as well.