First of all, the water doesn't have to be very hot to melt chocolate and butter. Both will melt in you hand.
Second, you are instructed to set the mixture aside. It's cooling down while set aside.
While it's set aside, you're taking the time to combine the flours etc. before to add the liquids. If you add them separately while mixing, any residual heat will be dispersed throughout the dry ingredients.
"If you want to make an apple pie from scratch, you must first create the universe." -Carl Sagan