You optimumly jet your bike to run its best when warm. When the bike is cold, the vaporized gas is condensing on the cylinder wall, creating a lean condition. The choke compensates for this by allowing more gas in (richer) per volume air. In other words, its getting you started; its not intended to be an ideal setting for a bike whose temperature is rapidly changing. As the bike warms up, it becomes overly rich until you shut the choke off.
I'm sure tolerances between engine parts that have not expanded to their normal operating size play some part in it too.