You're focusing on the trees instead of the forest, when the concept of canon is all about the forest. Yeah, when you're talking about a specific entry, of course its own details are going to be canon to it. But canon is about more than one entry at a time. Canon is about the series as a whole, otherwise there would be no point to defining a canon in the first place. This is especially important when discussing topics that span more than one entry in the series. Like if someone were to try and write down a canonical chronology of Samus's life from birth to the most recent story she's in, for any contradiction, only one option can be considered canon. In some series, like TES, you can maybe consider all options canon, because they make it a point to steep their lore in conflicting accounts, metaphysical mechanics, and ultimately incorporate the idea of contradicting facts all being true. But, for most series, canon isn't fluid like that. The author(s) intends one true account of events, and if this changes as the series progresses, that means certain conflicting accounts become non-canon to the main canon. That's what a retcon is. You can consider the outdated information to exist in their own offshoot canon, sorta like with the first Metroid, since it got overwritten by Zero Mission, but they're no longer part of the important canon. And some series might have multiple important canons, but they still have set events and facts. Star Wars basically has two canons, the one composed of the first six movies and all the EU content surrounding them (which most fans still consider the true canon), and Disney's new canon which only incorporates the first six movies, their nine movies, a TV show, and any new EU material created after this new canon was established (which Disney wants everyone to accept as the true canon). But Metroid hasn't done anything like that, so it has one main canon and a few offshoot canons born of retcons.
So, when it comes to Other M, there are two options. Either A, when it released, its account became the main canon. If that's the case, then most of the other games, at least as they previously existed, are no longer the primary canon (due to Other M's numerous contradictions to their accounts), and we cannot take them as in-universe fact, or use them to predict and discuss upcoming stories and games, because those new games would likely no longer take those older games as true in the series history. Or B, at some point, Other M became not part of the main canon. This could have been before it even released, or this could have been a decision later made by the people at Nintendo, most likely by not considering it when making new games in the series. In this case, while it can be discussed in isolation as one canon, and we may hypothesize what elements of the other games can be considered true to it, it in can no longer, if it ever was, be considered a part of the true timeline of events in the series.
You're taking a very loose and fluid definition of canon, when most people and discussions follow a much stricter one. Because what is the point of even having the term if everything is canon depending on what you're discussing and how? It's like the tumblrites that want gender to have nothing to do with sex, interests, appearance, or even personality, and be purely defined for a person by the person at an individual level depending on how they're feeling at any particular point in time. At that point, gender becomes a meaningless term, because whatever gender a person would be would tell you absolutely nothing about them, their gender becoming an arbitrary label with no real definition. And that's what you seem to be defining canon as, an arbitrary label whose definition changes depending on what you're talking about when you're talking about it, which makes it an ultimately meaningless term to use, as whatever is discussed as "canon" can change on a whim and has the durability of a sandcastle in the tide.