Summary of problems:
Modern species and fossil evidence all give us insight into evolutionary history, and of the sequence of evolutionary changes leading from the common ancestors of modern species to the modern forms.
Explore Evolution is flatly wrong to tell students "all we can say for sure is that the internal organs of living reptiles, living birds, and living mammals are very different from one another" (p. 139). We can say a good deal more than that, and it is irresponsible to so grossly misinform students. To justify the claim that there is not "much fossil evidence of the internal organs of any 'intermediates,'" they cite a 30 year old paper which provides no empirical justification of its claim. Even if the argument were true 30 years ago, it is decisively not true now.
The claim that "all we can say" is that various living species "are very different from one another" is laughably wrong. It is equivalent to saying that we know nothing about a classroom of students except that all people are different from one another. Everyone certainly differs, and it is definitional that all species are different. But science does not stop with a simple statement that differences exist. What differences (and what similarities) exist? What are the patterns of similarity and difference?
Biologists ask those sorts of questions, and evolution provides a framework for suggesting testable hypotheses to answer them. The variation among living species helps to show what anatomical structures can persist, and what forms might have existed as intermediate stages in the evolution of other living forms. The evolutionary branching process gives us testable hypotheses also about the connections between structures, so that we can make testable predictions about parts of a fossilized organism which weren't preserved. In that way, fossils can tell us much more than just what came first. They allow us to test predictions about what life was like millions of years ago, and how different modern forms came to be.
Few other parts of Explore Evolution are so clear in their contradiction of the book's stated aim of "inquiry-based learning." This passage actively discourages inquiry into the connections between living things, their fossil ancestors, and the processes influencing the evolution of life today and in the past.