What aspects of Diamond's evidence in Guns, Germs, and Steel do lay readers have to take on faith?
Unless readers are expert in all of the fields Diamond discusses, they must take essentially all of his arguments on faith.
For example, most readers of this book do not have any independent knowledge of the number of domesticable plants that were native to any of the regions of the world in prehistory. We have to take Diamond's claims about this on faith. Most readers do not have any independent knowledge of the various Polynesian cultures that Diamond discusses in Chapter 2. We have to take his claims about them on faith.
Of course, Diamond has sources for all of these facts, but he does not cite specific sources for specific claims. He does not write this book as an academic work with footnotes and specific citations. This requires us to take his arguments on faith unless we want to do research on our own.
Beyond that, Diamond's arguments about causation must be taken completely on faith because there can be no firm evidence to prove or disprove them. When Diamond says that culture plays no part in whether some cultures are willing to adopt technology, we have to take his argument on faith. There is no way to prove why some cultures adopt technology and why some do not. Diamond's arguments are plausible, but they cannot be proven.
So, lay readers must take essentially all of the book on faith because they do not many (if any) of the facts in the book independently. However, some claims that Diamond makes (those about seed size of ancient plants) are provable with research. Other claims that Diamond makes (that China rejected technology because they had no countries competing with them for dominance) can never be proven and will always have to be taken on faith.