I don't believe this was the twist Iwamoto was
referring to, but according to the recently added product description on
Rockman X: The Novels Amazon page, the book's plot is reportedly an adaptation of Iwamoto's
X1 manga.
By adhering to Iwamoto's 1994 adaptation, we can expect to see manga-exclusive characters and events in novelized form. For example, the opening moments of the manga throw readers in the midst of Sigma's uprising. Here, X finds himself at a moral impasse with an Irregular called Pierrot. X is unable to bring himself to off a member of his own kind, so Zero does the deed for him. A few pages later, X, to Zero's surprise, elicits an emotional response to a dog killed in combat:
he's actually crying. These early moments lay the foundation for X's character arc; the struggle of being a robot with human feelings.
There are currently no plans for an English language version of
Rockman X: The Novels. I don't doubt, however, the possibility of someone taking up a fan-translation down the line. In the meantime you should
check out Dr. Neko and Ayami Zero's X manga scanlation project if you haven't already. An oldie but a goodie!