http://www.uesp.net/wiki/Skyrim:Sithis
As you can see, this book is presumably the beliefs of the Dark Brotherhood concerning the creation of the universe. However two things are off at the end. First, the line "Go unto the Sharmat Dagoth Ur as a friend." Second, the chant "AE HERMA MORA ALTADOON PADHOME LKHAN AE AI", similar to a chant in the 36 Lessons of Vivec. And with the book claiming that Lorkhan was created by Sithis, I believe I have found something. Dagoth Ur was sponsored by Sithis, via the Heart of his False Aedra servant. Does this explain his actions? Is the Tribunal related to Sithis as well? Do they know of this? Also, why would this book increase your Alteration skill?
The book was made before the Dark Brotherhood was (publicly) known to worship Sithis, when everybody still thought they were just a less-scrupulous Mephala cult. I always assumed it was sort of a Dunmer Creation Myth, since they glorify Lorkhan and scorn the Aedra.
The final message, "Go unto the Sharmat Dagoth Ur as a friend" seems fairly self-explanatory, to me: As Lorkhan went to the Aedra, arrayed in glory and presented as like-unto-them, so must one confront Dagoth Ur... whether literally, Nerevarine-style, or as a metaphor by the Tribunal Temple (where Dagoth Ur was their "Devil").
I can't remember what the meaning of the final words is... something about "secret knowledge is the weapon of change/chaos" or something like that, but the Lorkhan part is new.