Changes in magnetic flux in small areas reduce the amount of heat that can convect to the surface - so those areas cool down slightly. ("Sunspots" are still blindingly bright; they are just slightly darker than the rest of the Sun.) Because it takes time to reach the surface of the Sun. Keep in mind that the Sun is huge - almost a million miles across. It is so large that it can take photons thousands of years to make it from the center of the sun (where fusion is occurring) to the surface.