Every LCD monitor screen is made up of rows and columns of transistors. The native resolution of the screen is when the resolution set by the graphics card (eg 1280x1024) equals the number of transistors. For different graphics card resolutions, eg 800x600, the electronics has to fiddle the screen so that 800 pixels have to map to 1280 transistors across and 600 pixels to 1024 transistors down. The result is that the display is slightly distorted and sometimes slightly fuzzy. Running the graphics card at the screen's native resolution gives the sharpest picturs.
It does the monitor no harm to run at a non-native resolution.
Clear Type is a way of making the fonts look sharper. That is why it recommends starting from the sharpest resolution, the native resolution.
Use whatever resolution is best for you - it will not damage the monitor. And if Clear Type makes like better, then use it.