Where would these settings be located? I'm assuming there's simply an RBG somewhere in some menu, but I can't find it.

I don't think there is. I know the background differs depending on whether you're using None/Bloom/HDR, and it also disappears when the console is open, but that's about it.

That doesn't make any sense. It has to be somewhere. Or is it built directly into the executable? My knowledge on how programming actually works is limited.

One of timeslips mods is a includes a replacement shader for that. You could extract the omod to see what shader it is I guess.

http://www.tesnexus.com/downloads/file.php?id=7332

A shader. Duh. Thank you very much, I'll look into it.

If you're talking about that ugly sepia background on the inventory screens, you can change it in the ini file - I believe it's bAllow30Shaders; set it to 0, and you'll get color.