Summary of problems:
As used in standard biology textbooks, "evolution" has several connotations, but they all derive from a single concept. Explore Evolution obscures the relationship between these concepts by treating them as three definitions which can be taken in isolation from one another. These definitions are not actually different ideas, just different consequences of the same idea. Attempting to divide these topics and act as though students can choose which to accept a la carte is a common creationist fallacy.
Full discussion:
In describing what we now refer to as "evolution," Darwin usually used the phrase "descent with modification," using the word "evolve" only once in the The Origin of Species:
It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the external conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone on cycling on according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.Charles Darwin (1859) On the Origin of Species, 1st ed., John Murray, London (facsimile edition, Harvard University Press), p. 490
In this concluding paragraph to the book, Darwin lays out the connections between the senses of "evolution" which Explore Evolution attempts to keep separate. Traits vary between individuals, and some of those differences can be passed from parent to child. Some of those heritable differences leave the offspring at a greater advantage than others. That process of natural selection can cause one population to become increasingly different, branching off from the ancestral population. Where heritable variation exists, this branching pattern of descent is inevitable, and it is possible to trace the evidence of that common descent back through history. Thus, the existence of change over time (first definition in EE) is part and parcel with the power of evolution to produce novelty (third definition in EE), and that change over time will inevitably produce a pattern of common descent (second definition in EE).
Why do we talk about universal common descent in particular? The most basic reason is that the idea of a single origin of life is the simplest explanation for the diversity of life that we see in the world today. A scientist who wants to challenge universal common descent cannot simply say that there may be something, somewhere, which doesn't share an ancestor with the rest of life on earth (as EE's "critics" do). That scientist would have to present evidence that a particular group of organisms does not share an ancestor with the rest of life, and show how that hypothesis is better than the hypothesis of universal common descent. Explore Evolution does not propose to replace a successful hypothesis with a better hypothesis, it merely emphasizes areas of uncertainty, but doesn't provide students with the knowledge or tools to gather new knowledge or improve our existing knowledge. Thus, the textbook fails both to accurately represent how science is practiced, but also a failure to live up to its claim of being "inquiry-based."