So after some further messing around, I've found that I can change the in-game settings by editing the registry, but I cannot set to anything that isn't in the video options menu. I also cannot set the color depth to anything other than 8-bit and 16-bit (I tried 32 BPP, then 24, then 15, 14, and 9, just to be scientific.).

So, as something of a conclusion, you can adjust the options by editing the registry, but it doesn't seem you can so anything in the registry that you can't do in the options menu.

Well, wasn't this a useful thread.