That could work, and it'd certainly make both the original creation and adding more options (if and when Toady implements them) easy, though it might not be the most user-friendly idea. Have you considered using tabs instead for the grouping? Of course, that'd make sub-groupings more difficult, but it might be worth thinking about.
Also, random ramblings:
I think the first step ought to be to draw up the different divisions you want to make in the settings, and think of how you as a user would like to interact with them. What would you find most comfortable? Don't think about what would be easiest to code yet, that can come later.
I'm more of a programmer than an UI designer, myself (and I'm not that good of a programmer, if I have to be honest, the years since college have taken their toll >_>). I'd offer to help like that, but all my serious "work-on-stuff" time is taken until the beginning of April. I might be able to help with punctual things, but that's all.
If you're still working on this in a couple weeks and haven't gotten past that point, I might have something I can tweak into parsing DFs config file style (I have something similar coded, but it does need some tweaking - and I won't be able to do it until the first week of September). If you're interested, that is. I don't know if you'd prefer to make this thing from the ground up yourself.