I would need to take some time to review the novel to really provide my answer as to what I think is the best course of action, but I remember having the impression that the novel abridged some events to the extent that they did not flow nicely, i.e. the pacing felt rushed and unnatural. There are parts of the game's version of events where it feels more realistic and therefore canonical by the sheer fact that there are more details.
Having said that, I would be uncomfortable relegating the game as non-canon. Before reviewing the novel, I want to list the various options we have before us:
- Write purely off the game, treating it as canon; novel's version in BtS
- Write purely off the novel, treating it as canon; game's version in BtS
- Compromise b/w the game and novel, giving priority to the game
- Compromise b/w the game and novel, giving priority to the novel
- Have a tabber system where readers can switch between the game and novel versions
- Give both accounts while using a unique template explaining that which version happened is ambiguous (Zero's suggestion)
- Treat novel's version as actual events, treat game's version as just how Layla experiences them (Lacrosse's suggestion)
So far, the option I have a slight preference for is (4). My main reason for this is that Ubisoft technically has said already that the novel provides the canon version of events; it is only that implementing it as such has proven less practical, to the point that it is hard to treat the novel's version as canonical unconditionally. The game's version most of the time just provides more detail which rounds out the story. Under (4), we would prioritize the novel's version in cases of irreconcilability, but in other cases, they would just supplement one another with their details. I think the potential flaw to #4 is that the resulting concoction of game and novel could ultimately be our own creation, like which details get expunged and which details get incorporated would end up being our design even if we are as precise about as it as possible.
(5) and Zero's suggestion are also viable alternatives. Despite Ubisoft's word that the novel is the canon version, I don't think we can be faulted for taking a step back and treating both the game and novel as ambiguously canon to be safe. These two are certainly the safest course of actions. My only concern is that #5 would be too complicated to implement in terms of coding and as for Zero's suggestion, I am not sure how we would organize the two different versions in the article.
For Lacrosse's suggestion, I'm not too comfortable because the game's version contains so much more detail that the logical conclusion based on this interpretation would be that most of what she experiences are artificially generated scenes made from nothing and not based on any memories at all. Her experience in the Animus would essentially be less exploring the memories of the Eagle Bearer and more exploring a mostly fictional world. However, an argument might be made that no matter how we spin it, it is canonical that Layla experiences interactions by Kassandra with Lagos that never took place in history, meaning that somehow her Animus or she herself really does just create false scenes to fill in broken data.