Ah, okay. There are certainly some valid reasons you might want to output to a different resolution, particularly when output is destined for a different kind of display. Perhaps it would be better though for these scenarios to be handled separately from the settings which define the physical size of elements. It has me thinking… I have my MBP hooked up to a 30 inch display. I wonder how the Retina MBP would handle that. I'm assuming it would handle it with all the grace and refinement I expect from Apple, recognising that the 30 inch display has half the resolution, and I would still expect UI elements to look the same physical size.
As I discussed in another recent comment, Apple's approach to UI design certainly makes many decisions to simplify things for (hopefully) the vast majority of users. The idea is that you put the settings that most users want to adjust front and centre, and then progressively tuck things out of the way which less people will want to change, and/or which they will only want to change occasionally. Mostly I think Apple get this pretty right, and I have always found Apple's settings to be far more logical than Microsoft's, but that's just my subjective opinion. One example where I think Apple got it wrong is with brightness setting on the iPhone—adjusting the brightness manually is something I find myself wanting to do a lot, and it's a little frustrating to have to go into settings every time you want to do that. I guess you're saying that some settings you wish you had simply aren't there at all, and I can understand how that would be frustrating.