Summary of problems:
Common function can explain certain similarities of form, but cannot explain similar developmental pathways, or the particular components that make up certain structures in different species.
Full discussion:
The discussion of functional constraints in Explore Evolution is nearly impossible to state in a way which does not refute itself. They do not deny the remarkable similarity between the structures of species within various taxonomic groups. They do not deny that one can produce a hierarchal (branching) arrangement of the ways these structures vary within and among these groups, and that the branching pattern is consistent regardless of which particular structure you examine. In other words, their response to the evidence of the branching pattern predicted by the tree of life is to agree that it is all accurate. They simply argue that it is possible to invoke special explanations for each such structure, multiplying causes needlessly. This practice violates basic scientific and logical principles. By treating structures in isolation, they obscure the actual evidence examined by scientists.
For instance, EE cites biologists from 150 years ago, biologists whose arguments were tested and found lacking.
Agassiz, for example, explained homologies as the result of the necessity of using similar structures to solve similar functional problems. On this view, the pattern we see in the vertebrate forelimb a single bone closest to the trunk, two bones in the next segment, and a variety of bones in the segment farthest out exists for important functional reasons.EE, p. 43
It is worth noting, to begin with, that vertebrate limbs do not have "a variety of bones in the segment farthest out." The number of fingers and toes is consistent. The numbers of bones in each finger and toe are consistent. The number of wrist bones is consistent. Even if functional constraints could predict the broad pattern, they do not explain why no living species has more than 5 fingers or toes, nor the consistency of the number and developmental histories of the wristbones.
Furthermore, functional constraints do not explain the broad pattern. Robotic arms do not typically have one element nearest the base, two further out, and a number in the "hand." They employ various sorts of joints and connections which do not exist in living species. The argument of functional constraints only make sense if you assume some evolutionary process acting on some common starting point. That explains vestigial fingers and toes in the legs of deer, it explains why our two legs, and all four legs in a deer, still have two bones in the middle segment, despite having no need to twist. It explains why no species has more than five fingers or toes, and why vestiges of all five can be found in vertebrates which seem to have fewer. These results would be surprising if there were not some common starting point, but are predicted and found because of evolutionary hypotheses.
Wing morphology: Pterosaurs, bats and birds produced wings with functionally similar shapes from a homologous organ (the forelimb) in three distinct ways. The bones in each wing are homologous, but because the different arrangement of bones within the wing, the wing itself is independently derived within each group. Image by J. Rosenau. The claim of consistency because of functional constraint also does not match the actual evidence. Because of the basic physics of flight, bird wings, bat wings and pterosaur wings must all be similarly shaped. If they were shaped much differently, flight would be (or have been) impossible. If the functional constraint hypothesis were the sole explanation for wing structure, we might predict that all three types of vertebrate wings would be similar in their anatomical structure, but this prediction fails. Pterosaurs have a wing consisting mostly of skin stretched between the 4th finger and the body, with the thumb and three fingers free of the wing. Bat wings consist of skin stretched across all 4 fingers and attaching to the leg, with the thumb free of the wing. Bird wings (like chicken wings you've eaten) do not have skin stretched across them, have fused the bones of the 2nd and 3rd fingers together for strength, and cover the structure with feathers.
Within each group, these traits are consistent, indicating that the wing can be treated as homologous within each group, but not across groups. All three wings share the same bones (the bones are homologous), but they are arranged very differently. Bats use all four fingers in the wing; birds use two, have lost one finger almost completely, and another is nearly functionless; pterosaurs used only one finger in flight, but adapted other fingers to different purposes. Since the anatomy of these wings is so different, this falsifies a prediction of the functional constraint hypothesis.
It confirms what we would expect from evolutionary explanations. Because vertebrates share a common ancestor, all three groups shared ancestors which possessed the basic vertebrate limb. Each group took steps toward flight at different times and from different ancestors with different initial traits. The differences in starting conditions meant that different sorts of genetic and structural changes were advantageous in each different group. Within each group, the structure of the wing is consistent, indicating common descent within pterosaurs, within bats and within birds. The differences in the structure of each type of wing indicates that wings evolved independently in each group. The similarity of the bones in the wings (and elsewhere in the body) indicate that all three groups share an ancestor farther back in their history. This nested pattern of shared characters is exactly what common descent predicts, and has not successfully been explained by other means.
Functional constraints cannot explain why vertebrate wings should consist of skin stretched over bone, since birds do not use skin for the flight surface. Indeed, insect wings do not have bones or skin, and are not derived from legs. Insect wings are structurally similar (homologous) to gills. Again, this pattern of similar structure is unexpected under the predictions of common functional constraint, but entirely predictable based on evolution and common descent.
An inquiry-based textbook could turn a discussion like that above into a fascinating exercise. Students could generate predictions based on various potential explanations, and then test them using data from various biological structures. Explore Evolution, despite its claim to be inquiry-based (and despite the nonsensical and meaningless exercise on pp. 46-47), does not invite students to examine any evidence at all, nor does it explain why students should ignore the research conducted in over a century since Agassiz defended his position. Inquiry-based instruction invites students to discuss the topic, but no useful discussion could possibly proceed from such a flawed foundation.