>>54995247>>54995293When it comes to legendaries a good way to know if the catch is canon is if it's mandatory/made with a changed catch rate. For example, Dialga and Palkia don't have changed rate in Legends, but you are forced to catch one of them, then the other one, as Origin Palkia/Dialga is also forced to be captured with 100% of success.
Eternatus and Ogerpon are also 100% rate captures. In ORAS, Rayquaza got its catch rate changed too because catching it was part of the Delta Episode plot, but Primal Groudon/Kyogre weren't, since catching them isn't part of the story in any way, you just have to stop them. Back in XY and BW, the dual legendaries also had to be catch, unlike Groudon/Kyogre, but like Rayquaza, Eternatus, etc.
I would say Legends is the odd one, since you really have to catch all legends to complete your mission with Arceus (hell, you even have to catch many to fight Volo), but like Cogita said, the protagonist will eventually die and those pokemon will be free so Rei/Akari completing the Hisui dex isn't really a canon issue, they all become wild pokemon by the time the other Pokemon games take place.