Outstanding work, sir. Major props to thoroughness.
I think I closed my mind off when I read it. I only noticed a handful of descrepancies when I read it, but they would only be descrepancies based on what source the reader chooses to christen the truth.
I think Hasbro, when they commisioned this book, acknowledged that their cash cow had reached so many people through different incarnations that it would be IMPOSSIBLE to establish a true prequel to all versions of Transformers, so it focused more on producing a solid origin that honored what, in my opinion, most fans have declared their favorite approaches. [Plus the author is left to add his own favorites, which Alex mentioned in a recent interview].
Once again, only opinion, but I loved the book because it incorporated or acknowledged the main canons. References to Six Lasers Over Cybertron [Beast Wars], The Quints, Unicron, Orion Pax, the Wreckers, and I think they mentioned The Elite Guard, too. Ratbat was his G1 comics version I believe, Prime his Dreamwave War Within version kinda, and I think the simmer to a boil approach to the Prime/Megatron war of ideals rocked. it gives something from our childhood an awesome dramatic weight.
I know this thread's for focusing on the differences and not opinion, but I think DK's Ultimate Guide by Simon Furman should be due for a revision and they should ask you to work with him.