Regarding the other example, you are assuming that the Encyclopedia, just because it sometimes backs up the novels and not the games is the one that defines what is canon and what is not, which I think is wrong, since the games should always be the top tier regarding canon.
For example, in the Encyclopedia, it says that Sofia Sartor was born in 1473, while in the Assassin's Creed: Revelations database it is said that she was born in 1476. I think that we should always go with the information presented in the games, and everything that contradicts it should not be considered canon.
With this said, I don't even know why they contradict themselves so much regarding this kind of information, even if this information is considered trivial. Take the example of Sofia's birth year for example. I think they should take your advice Sima, and hire someone to keep track of all this information, in order to not cause confusion.