It's not so much as having the inverse for the sake of having the inverse, but rather to compare both colours. If you just have the background, then civs with a similar background colour seem too close, but when you've got both you can compare them and see they're different enough. Polynesia and the Maratha, for example:
Despite having similar colours (they're the closest I could find on short notice), having both there side-by-side shows how different both the icon and background colours are from each other, while clearly showing background and icon without confusion between the two in a way that's easy to reproduce (I've got a .psd template that just requires changing the colour overlays, placing the 256 icon file and changing the civ name) and clear to read. If you like this, I've got some time now and can whip through the vanilla and More Civs civs, as well as any others where the author gives me the 256 sized icon (and RGB values if they want to be more specific)
EDIT: And this is why I hate fast moving topics. I still think we need a solid version of the icon colour, since it's hard to compare them when it's just the text. But that's just my opinion.