The headline is misleading, the resolution is 2880x1800 on the retina model. The setting changes how large the UI elements are, only.
All fixed pixel displays (which includes all LCDs) always render to the full resolution of the screen, assuming there is no letterboxing or pillarboxing going on (which is the case for all screen modes offered by the OS for the MBP).
So what you've pointed out is absolutely true, but it is also elementary, and misses a big part of the story.
When the OS is set to a resolution that is not the native resolution of the display, there is - by necessity - a scaling operation that must take place when rendering the frame buffer to the display. This operation a) costs some time to perform and b) can lead to undesirable image artifacts. This, by the way, goes far all OSes and all non-native resolutions (for fixed pixel devices), not just the new Retina MacBook Pro.
Now, what apple has done is given you two choices. Your first choice is to let the OS use a 2880x1800 frame buffer. This is the "Best for Retina display" option. You avoid hardware scaler (in terms of the rendered frame buffer). The thing is, in this case, you are locked into fonts and other graphical elements rendering to a pixel doubled virtual resolution of 1440x900. Retina aware applications can certainly choose to render graphical elements and other content to the full 2880x1800 resolution. A 1080p movie can render in a 1080p window. A game can render to 2880x1800. So that part is great. Still, your text, buttons, and other UI elements are larger than necessary.
Maybe, because that last part annoys you, you decide that you will opt for the other choice apple gives you - "Scaled". You can now pick your resolution from 1920 by 1200, 1680 by 1050, 1280 by 800, and 1024 by 640 according to Apple's website. Notice that all of these are 16:10 aspect ratio so there will be no letterboxing or pillarboxing. Now, in this case Apple got tricky. They tell the video card to render to 4x the selected resolution so that, before the scaler does its thing, you are starting with an image that is 4x what you want for the final result. This helps combat scaling artifacts - you are giving the scaler 4x more information to work with than it would otherwise have. This is great, but it won't eliminate artifacts completely. Also, remember, as I said earlier, this scaling operation takes time, as does rendering to the very large screen buffer (larger than native even, for the 1920-by and 1650-by resolutions). And these tradeoffs are exactly why the control panel offers the disclaimer "using a scaled resolution may affect performace"
So what can be done to improve the situation? First off, what apple could have done here (and may do in the future) is for the first choice, have a checkbox that says "Use full-size UI elements" or something along that line. By default this is checked. If you uncheck it, you get the result as shown in the article - very small text. As many point out, this option is less than useful for most people, and that's why Apple probably avoided it.
But what if instead of a checkbox, they gave you a slider? This slider would control the virtual resolution (really, the effective DPI) that the OS uses to render UI elements. "But", you might say, "that's just going to make everything look bigger, and they already gave you that option with the scaled resolution options". And you would be correct. However, by doing it this way, you allow the OS to draw individual graphical items at the correct size to begin with. You are painting the picture (rendering the frame buffer) the same size as the screen from the get-go, and avoiding the final scaling operation you'd have to perform otherwise.