The fundamental 'issue' here is that gaming history is, ostensibly, two different things which this article, and many in this thread, are touting as the same thing:
The 'Popular' History. Or, the history of how the wider public experienced games as the industry developed. This is inevitably going to focus on the biggest player/s. Which, in this case, means Nintendo gets a
lot of focus. Whilst that's different for places such as the UK and much of mainland Europe, there's no stopping the fact that Nintendo has, ultimately, been dominant throughout much of gaming's history. Whether that be through mindshare, or the simple reality of them usually having - at the very least - one truly mass-market console and/or handheld on the go.
Though I don't think Nintendo specifically is that significant of a factor. Look at
the list in this thread, or really
any major gaming awards shows of the past 20 years, and you'll find that Nintendo tends to take a far smaller role in overall discourse than you'd really think given how consistently massive their titles are sales-wise. In your typical 'gaming circles' (like this one, really), it's genres like the action RPG, or developers such as From Software which take a near-overwhelming amount of the discourse. The vast majority of games, whether by Nintendo or otherwise, simply do not get much of a look-in outside of their own respective niches. Which, personally, represents a far worse 'shrinking' of the 'popular history' than that which perhaps-overly bigs up Nintendo's long, and frankly far more varied, history of releases.
The 'Academic' History. This is a lot more muddy because, frankly, the gaming industry simply does not care to examine its own history all that much. Developers rarely - if ever- talk about other game influences in any meaningful way (and that's before how the business side of things inherently messes with continuity in artistic visions). The dire state of videogame preservation makes the simple matter of accessing historical works difficult. Culturally, gamers have often balked at ideas that aim to view gaming history through an academic lens (see; the backlash towards 'ludonarrative dissonance' as a concept).
It all just leads to cases where, instead of trying to find some academic idea of 'how gaming developed', people just shout over each other about how their own version of the 'popular' history is more 'real' than others. Usually evoking the idea of "what did what first." Which, sure, is a good basis for historical analysis, but it's really just that; a basis, and not an actual conclusion. A chronological timeline of what features debuted in which games says very, very little when it comes to how those features actually did - or did not - impact the history of videogames.
So, whilst it is probably true that Nintendo is over-represented when it comes to the 'historical canon' of videogames... said history has been neglected so much by both game-makers and gamers themselves that, frankly, it's kind of implausible to say how said over-representation asserts itself. Saying "Croc was a 3D platformer before Mario 64, so Mario 64 is less culturally relevant," is, fundamentally, just saying that you personally don't care for how beloved Mario 64 is. It's really just going to boil down to a matter of opinion at the end of the day. Which, yeah, this article kind of is.