I asked that question, and let me make my case for it.
The Assassin's Creed novels are, well, novelizations, and accordingly, there are constraints on the author:
- The IP owners may have their own desires and ideas about how the series would evolve, which the author might have to respect. Indeed, an unlikely hypothesis is that Ubisoft want the modern-day events to be combined in a single novel.
- The fans may have an expectation that the novels will be faithful to the original, and indeed expand upon it.
- The author may not have control over how the series will evolve, so every change made would have to be made keeping in mind the need to compound that change in the future.
Any point of difference in the novels is not merely the will of the author.
In fact, differences like this are things I would expect one or more of the following to comment on:
Now it's certainly possible that nobody has commented on this yet. But this is a significant change and it must certainly have been discussed, if behind closed doors. We may never know, but that is no reason why the question shouldn't be asked.