There is in actuality very little canon storytelling in the StarFox series when compared to almost any other game. The entire 'story' is essentially flat and it has been fleshed out (often plausibly) by the community. The game is a shooter, and stories are often an afterthought in games of this genre. StarFox has it's inconsistencies, which shows this. The fact is simply that the story is not why you play the StarFox games... it's not meant to be story heavy... it's not final fantasy or metal gear solid. Gameplay has been the focus, and what ever "deep" story anyone get's out of it is only because of gamer culture adding plausible theories.
Additionally, its really hard to convince someone that something is truly canon material, unless it appears in the game; arguing will get you nowhere. Stories are changed in the translation process... you have to just take it for what it is and realize that there could be plot holes... I mean, its clear that the story of "StarFox" isn't the most fleshed out piece of literature/writing we've ever seen.
Take it for what it is. A simple game, with an entertaining story added. All these tiny minutia (while interesting for speculative debate) can't be proven until it shows up as a primary theme in the game (or is made clear in game). Instruction manuals have had tons of conflicting information, because often times the people writing the story are different from the people drawing up an instruction manual. It's often filler that's never even touched in game.
Originally Posted by Scourge of Ages
2nd: It's spelled canon. Cannon is a big gun.