EDIT: Ok now we're getting somewhere!....Er, kinda...now my ship (started with the Vasari's new capital ship, whatever its called) turned completely orange.
Okay, I thought that might happen. Basically if you don't have an alpha channel the game treats it as being completely 255 (or white when represented as greyscale). The alpha channel is team color, with the 0-255 alpha value in each pixel indicating how much the team color should be merged with the texture. Since its all 255, its all team color and none of the original texture.
For quick tests, you could just make a new image, paint it totally black, copy it, go to the texture, and use alpha mask again. Check use from clipboard, and the image should go totally transparent (I.e. no team color at all). This should allow you to see your changes.
For the final product, you'll probably need to find the extract channel plugin (that might be part of a package), get the original alpha channel as its own image, copy that and apply it to the finished RGB texture.