The reasoning is to allow the yeast to settle so that you can get rid of most of the liquid and just pitch the yeast. However, if you don't have an enormous starter, like for a lager or high gravity beer, I have heard it is best to pitch the starter at high krausen so that the yeast are healthy and active when you pitch. I don't remember the percentage rule of thumb for how much starter beer is ok to pitch into your wort, but if its a 1L starter for a 5 gal batch I will pitch the whole thing at high krausen.