I can't see the endorsed novelizations as much more than glorified fanfiction in themselves.  They're relatively well written, of course, and rather accurate, with small changes for a more read atmosphere.  The discrepancies between both novels to one another and to the movie itself are understandable, if not always to my liking.  Neither are very creative - they do tend to stick close to the movie, with the "adult" version being more flexable.
 

The first novel is entitled Final Fantasy: The Spirits Within, understandably.  By Dean Wesley Smith, an author in his own right who has a background in science-fiction.  By his dedication note, I could say he has some bacground in table-top gaming as well, but I digress.

It looks as though the book's cover has variations by edition (there seem to be at least three on Amazon's Japanese 'site).  There is also a digital, E-Book version.  The cover of the book I have is of Aki standing in the path/wake of the light, with the facebacked letters and "The epic novelization of the stunning cinematic blockbuster" printed in small letters along the top.  The publisher is Pocket Books and runs two hundred-thirty pages.

The back cover reads -  Earth, 2065 A.D.: Destruction and confusion are everywhere. Cities are deserted, the population is decimated, and the few humans who remain struggle to survive against an insidious alien presence that is consuming the very life energy of this wounded world. The presence is spreading across the planet, infecting everything in its path, killing the Earth one life at a time.

Only Dr. Aki Ross, a brilliant young woman haunted by dreams of death, may hold the key to saving the world. But her plan is not without its risks, and a rogue general commanding the most technologically sophisticated army in history will storm heaven itself to stop her if he has to. He has plans of his own to stop the alien life force in one decisive stroke...plans that will stab at the very heart of Nature itself unless Aki's quest succeeds.

I can't be sure how learned the author was in The Spirits Within's world.  He does seem to have a good hold on some aspects, but he also enforces a lot of creative license.  The names he uses for characters not named, for example, are now typically considered to hold true by most, but I can't help but wonder....
 

The second novel is entitled Final Fantasy: The Spirits Within... and I guess there's some logic in that.  By John Vornholt (also a writer with a background), though it's advertized as by Esther Friesner on Amazon.  Huh.  Anyway...

I don't think this one has variations in publishing, but the cover is the same as my Smith edition - Aki in the path/wake of the light, facebacked letters for the title.  Instead of "The epic noveliz..." along the top, it's a "Can Aki save humankind - and herself - before it's too late?" below the logo.  It, too, was published by Pocket Books, but under a subdivision as A Minstrel Book and with no kangaroo in sight, and runs one hundred-thirty-two pages.

The back cover reads: Earth, 2065.  Destruction and confusion abound.  Cities are deserted, the population is decimated, and the precious few humans who remain must find a way to survive.  All are threatened with their mortality on a daily basis.  With life and death already defined, humans are left to discover their hearts and fight for their very existance.

Aki, a confident scientist, is one of the survivors.  Her mission is to find a cure for the planet, which is under constant attack by a predator.  But powerful forces oppose her work.  It is crucial that Aki succeed: the fate of humanity rests on her research, as does her own survival....

Vornholt writes clearly many of the "unintelligible" parts of the movie, and it's still understandable, even though it really was written for the younger audiances.  It even comes complete with sixteen glossy colored pictures in the four pages between pages 88 and 89.  In some ways it mirrors Smith's rendition (or vice versa, or even...) and in some ways it goes off on its own.
 

Not to ramble on and on, but I figure I'll give a referenced overview entirely from mine.

In all likelyhood, I doubt that either author were prepped more than with a script and screening of the film, if one didn't play off the other entirely.  Regardless, taking any given scene and comparing them, we can see the differences between both the authors' takes and the film.
 

Taking the Trio's part in the gondola scene, the differences are evident:

The movie keeps the balance - Jane catches Ryan and Neil up to no good.  Wandering up, she announces herself and demands an explanation at the same time, keeping a distance.  She seems surprised Ryan would be behind such a scheme, as it turns out, and Neil finishes his work as they're talking.

In Smith's embellished version, Jane manages to sneak up on them until she's, quasi-literally, right on top of Neil.  She makes her presence known by speaking directly into his ear, where it's further hinted (following a few paragraphs earlier) that he's difficult to sneak up.  There's diaglogue, in which Neil jumps in for attention rather than trying to pawn off responcibility, and Ryan points to Neil as the mastermind.  Following the implication, Neil makes two cryptic remarks to Jane, who gets violent thoughts before being cooerced by Ryan to help (as in, "not hinder") their plans for Gray and Aki.

Vornholt's text is much simpler.  It scripts the movie mostly, except Neil is on a platform above where Ryan is.  From there, he spots Jane coming and has the first word.  Jane is disgusted, apparently, but Ryan tries (only tries, as we don't see how successful it really is) to make her see things their way until Neil finally breaks the gondola, and procedes to shout his success to the world.
 

Sometimes we all pretty much agree.  Taking from two paragraphs near the end of the books:

Smith: "The closer she got, the more she could tell he was hurt badly.  Blood was dripping from the corner of his mouth, and his eyes were rolled up in his head.  His breathing was shallow and raspy.  He clearly had internal injuries.

Vornholt: "Fighting back her emotions, Aki pulled the captain to his feet.  He staggered for a bit, but managed to stay upright.  From the trickle of blood on his mouth, she realized he must have more serious internal injuries."

Something I assumed from the film, but good to know there were a second and third opinion out there.
 

Lastly, the voice of the books are, as I've said, geared towards different ages.  Smith is descriptive.  And he took the soldiery in a more "adult" speach pattern.  They curse and take certain names in vain.  Or at least they do so more frequently.  Vornholt's rendition seemed overly simplified and there was much less cursing.  Oh, and Hein crowed.  And could see San Fransisco from his office window, apparently.
 

The Final Word?  Both books are entertaining.  Personally, I wouldn't use either for reference on TSW's inner workings, but they're good enough reads.