You can always edit the color palette with some skill. I myself managed to get a decent color palette with about a weeks worth of a couple of hours work (whole palette, not just one color). The only colors you can edit easy are player colors. You'd need to edit the art file to edit other colors and I suspect desyncs too (having a diff color.bmp does not cause desyncs, it's just that you see player colors as your own palette shows them).
I will let Hooman, or anyone else who knows the game system to explain why you can('t) add player logos and the likes (heck, you can't add a single thing to OP2, you can only edit, pervert,etc. Yes, you can add techs to the tech files, but that has a limiting factor to it).
As an idea for an OP3. Do we still have an actually active OP3 project?