Proof number four is similar in substance to previous posts in so far as it makes certain assumptions, specifically the assumption that God interacting with the world would look like magic. That God, if he were to do anything, that He would not use a natural phenomenon to accomplish the desired result. For example, it seems that GII believes that if for some reason God desired to destroy a certain building, it would only be done in a magical way, that it would simply collapse for no observable reason. It seems to be assumed that God would not use or, to turn a theistic phrase, ordain the building to fall by causing a number of circumstances to obtain, such as years of basement flooding, termite infestation, then a mild earthquake or hurricane to bring down the structure.
Proof Number 4: Think About Science
GII again begins the proof with their “Prayer List” objections, this time applying it to the illusion of being cured of a disease or sickness. Proof number four ties up the bulk of its text with a brief recounting of the accidental discovery of penicillin. How the scientists were not necessarily seeking to discover it, but rather stumbled upon the anti-biotic by a case of accidental genius. GII concludes:
Did Fleming or Floring say, as a religious person would, “The death of this bacteria is a miracle! God has reached down and killed it!” Of course not. Instead, they completely ignored “God”. They determined what was actually happening through experimentation and then made useful medicines from the mold. They took a rational approach rather than a religious approach and we all benefit from penicillin and its many derivatives today.
All of science works in this way. Only by assuming that God is imaginary and prayer is meaningless can science proceed.
The reason why scientists must assume that God is imaginary in order for the scientific method to work is because God is imaginary.
I will admit that I do not know every religious person, but I think it would be safe to say, I do not think many religious people would conclude a miraculous event took place. I reiterate, GII assumes that God has not had a hand in the formulation of the physical world. The Teleological Argument for the existence of God deals with this principle. God, as Creator of the universe has the power to work within it. There is no reason to believe that if there are laws of physics which were determined at the creation, are in place, that the universe would not conform to the structure of the set parameters. It is no surprise then, that people discover the way they world works. If the universe were not governed by cosmological constants it would be utter chaos. A belief in God in no way undermines the idea that we can explore and discover our environment.
It simply does not follow that because there is a world to be discovered that God does not exist, or that He is not necessary. The universe is so finely tuned, the probability it all came about by chance is so astronomical, that it is statistically impossible.
Sifting Reality 
I’m not one hundred percent certain that I’m remembering what Craig said correctly, but I think his position on this is that in science, we’re not so much assuming that God is imaginary as we are ignoring the fact of his existence. God is simply not relevant to a lot of the things that scientists discover. For example, if a scientist was trying to discover the chemical composition of water, it would not help him at all to bring God into the equation, so he can ignore the fact that God exists for the purposes of that particular inquiry.
As you say, though, the case may be different when it comes to things like the origin of the universe. Perhaps we do have to posit God to explain the beginning.
Good point, there is a difference between presuming non-existence and setting aside the need for divine intervention. Since the universe was created with a set of physical laws it can be expected to act a certain way without God’s active interaction.