I guess we'd also have to ask why certain individual languages (like Navajo) have verb rules that are even more complex than nearby "peer" languages such as Hopi, which was spoken in some of the same geographic areas as Navajo. Hopi verbs are complicated, but that language is regarded by linguists as easier to for outsiders to learn than Navajo.
As for the Navajo grammar book, you can preview parts of it on Google Books:
The Navajo Verb, by Dr. Leonard M. Faltz
I rather suspect the writer of your Navajo text may have fallen into the same trap. Maybe he learnt grammar from Kennedy's Latin Primer and now he wants to describe Navajo in a similar tome.
Well, he studied Navajo for decades; I think he's using the verb as a window to describe the whole language, since so much of Navajo is encoded by verbs. Nouns get rolled into verbs. I've seen Navajo verbs described kind of like this (though this particular example is general and may not be grammatically accurate):
In English, you would use a sentence like "She picked up the things," and "things" might be any noun. Eg, "She picked up the sticks" or "She picked up the flower" or so on. The noun at the end of that sentence leaves the other parts of the sentence intact.
In Navajo, most or all of that information gets encoded by a single word which acts as a verb. The literal translation of such a verb might be something like "The act of a female human bending down and retrieving two stickish objects with her hand, with the speaker as the observer."
If you change any part of that (with a third party as the observer, with a male human, with three sticks rather than two, etc.) the whole verb changes.