I have the scorcher theme on the Monarch, but it is not there when I leave subway town. In the garage when you enter from subway it shows starkies theme. when you return from the wasteland you can see the scorcher theme in the garage. The only time I can actually see it on the car during gameplay is when I return to disc 1

I thought the same thing at first and then I damaged the car and I saw it.

If you have the extra armor on the car then the armor has its own paint scheme but the car itself, which is underneath, will have the theme.