Board Thread:Wiki Discussions and Support/@comment-1783334-20150413163728/@comment-945885-20150414193928

The storylines for the Ninja Escapades in Storm Revolution, which provided backstory for the Akatsuki and Shisui, were supervised and edited by Kishimoto, so you could probably consider them canon (especially where they contradicted the anime version of events). I wouldn't be surprised if the upcoming Akatsuki Hiden novel features a similar storyline.

Otherwise, no, I don't think any of the other storylines in the game could be considered canon, beyond the idea that the games have their own internal consistency.