The scientific method is the best way we have to understand the universe?

Sara Passmore who is the president of the Humanist Society of New Zealand says:

The scientific method is the best way we have to understand the universe.

I often hear people say this, especially scientists.  The problem here is that the word "understand" in this context is ambiguous.

Let's consider an analogy. Is the best way to understand a computer game to play it?

Well, it depends what is meant by "understand". By playing it we come more proficient at the game, we can predict more readily what will happen when one's character carries out certain actions. But no matter how often we play the game, one will never understand why the game has the particular characteristics it has, nor why it exists in the first place.

Likewise with science.  The purpose of science is to map out the patterns discerned in reality and calculate how the world changes with particular actions on our parts.  But that's all it does.  Science tells us nothing about the underlying machinery of reality. It tells us nothing about how or why the world exists at all and why it has the particular physical laws it does. That is what metaphysics deals with.

So, when people say "the scientific method is the best way we have to understand the universe", do they simply mean "understand" as in the patterns we discern in reality and the way they change? I don't think so, because often people who say this are atheists and seem to be insinuating that science offers an alternative explanation to "God" as to why there is a Universe at all, and why we exist etc.  And this includes prominent scientists like the late Stephen Hawking, who really should know better.