When asked about the canonicity of Star Fox Command in relation to its predecessors (those in particular being Star Fox 64, Star Fox Adventures and Star Fox: Assault) in a Reddit AMA, Dylan Cuthbert had this to say:


In turn, many within the Star Fox fandom figured that he was implying that the game itself was not canon to the previous installments. However, years later, Cuthbert would clarify on what he really meant by Command being an "alternate timeline kind of game":


In reality, it seems what Cuthbert really meant was that each playthrough and story path is meant to represent an alternate timeline, not that Command itself was in a separate timeline from 64, Adventures, and Assault. Nintendo Dream's guidebook for Star Fox 64 3D from 2011 would actually include an entire chronological timeline of the series up to that point, beginning with Star Fox 64 and ending with Star Fox Command.

Essentially, all of the game's branching story paths are canon and non-canon at the same time, as there's said to be no true ending as it's up to the players to decide how Command, and perhaps the entire series' chronology as it truly began in 1997, ends. A 2011 Nintendo Dream magazine interview with Dylan Cuthbert, as well as Takaya Imamura, would reiterate this sentiment.