I’d worry that duplicating the option, like those crazy multiple light-switches on either side of a room, would just add further confusion. Do I set it here? Oh, I should set it here! etc. and the user doesn’t understand why it’s not working at the end of the day. Additionally, maybe this isn’t the same as ptram suggested, but Keith seems to have implied that putting the option in the Customizable Colors pane wouldn’t work:
I was vacillating. To be truly serious, I think the Pro version should be the regular bundle and users should pay extra for the simplified version, thus saving me money. 
In total seriousness, though, while the idea may have merits, I don’t think it really fixes the issue, which is that once users do want to customize something, they get overwhelmed by the options (and think of the stink that might arise once they found they’d paid extra for that confusion); and if they have no options whatsoever, they get grumpy that they can’t change “this one simple thing.” Perhaps if there were a middle ground, where it weren’t completely “Keith-default, no way to change anything” there might be enough customizable settings to satisfy a large user base–but then which settings should be fixed and which allow change? At a guess, though users on average may change only a few settings, those few settings will be different for a lot of people.
An “advanced” tab seems like a decent idea except that how do you organize all the “advanced” settings, even assuming you can decide which they are? Right now, the entire Preference pane is “advanced,” but it’s organized into Navigation, Appearance, Formatting, etc. Would the “Advanced” tab have that same break down or jumble everything together? The latter seems much worse than the design now stands, and the former just duplicates so much unnecessarily. Maybe leave it as it is and instead of an advanced tab there are “advanced” settings hidden via a disclosure box, a la the Compile settings?
None of this gets away from the main point, though, which is that once you do get to those “advanced” settings, whatever they are–and in all likelihood, a lot of users are going to try it at least once just to get that one setting that isn’t the way they want it in the default–there are a lot of possibilities and someone is going to get confused. You’d like to think that having clicked the disclosure/advanced tab, they’re agreeing to some kind of contract accepting that they’re going to have to read some manuals and do a little more work to understand the features they’re now making accessible, but people being people, I don’t think that’s something to count on. And even with a manual, some people just need it broken down another way before it clicks.
Right, I’m going to stop speculating and go pretend to be productive.
Edit
They have to check a box that says they’re over thirteen and then digitally sign it with their PIN so that we can track them down and sue if they whine. What do you think?