Good question.

Some parts of the inconsistency feel more like actual diverging timelines, while others feel more like conflicting viewpoints.

For example, in the different canons we have for the Legacy timeline we see at least three or four different versions of what occurs in the scene where Clu starts the coup and attacks Flynn and Tron.

Those definitely feel like different characters’ viewpoints, with the objective truth being somewhere between them, probably (none of them 100% correct, but all containing elements of what happened).