So, Cerny is acting purely as a messianic figure on the project, then?
Anyway, Shu's recent interview actually gave a very sensible depiction of how events worked: the game, from an artistic and design standpoint, was virtually finished years ago, but the hardware was not capable of making it happen. The decision was made to move it from PS3 to PS4.
Very little about the design or art changes as a result of this. That means years of technical work where the designers would be doing next to nothing. Rather than doing that, Ueda takes a leave of absence to work on other projects while the programmers complete the almost purely technical procedure of rewriting the code for PS4. This is absolutely normal; designers usually move onto a new project months before the game is finished, but in this case it got extended to years before it finished because of the extenuating circumstances of needing to almost completely rebuild the engine from the ground up for new architecture.
Mark Cerny is brought in to consult during this period because no one actually has experience programming for the PS4, so he's the closest thing to a subject matter expert you can find. This is normal, especially for small teams where many of the members may be highly specialized in working with specific sets of hardware and need training on programming for different platforms.