Of course, Halos 1, 2, 4, and 5 all began or ended with the Chief helmetless (honorable mention to "Reach" doing it at both ends with its protagonist). It's not a religious thing, it's not even an in-universe thing, in non-visual media, he walks around like a normal person all the time (and even the visual depictions have been gradually pushing the line back on how old John can be before we stop seeing his face). It's an affectation within the games that the audience (and the audience alone) never sees his face, that only works because they're mainly in the first-person and mainly set when he's on-duty. It was pretty much a dead issue from day one, Bungie clearly wanted the Master Chief to be a nameless, faceless vessel for the player, like his spiritual ancestor, the Security Officer from Marathon, or his to-the-extreme descendent, Noble Six, but that went out the window when Microsoft demanded a prequel tie-in novel that gave him a name, a physical description, and a life story regardless of any plans the actual developers had, and the book sold well enough it couldn't just be ignored. Once that happened, you may as well show the man's face, you've given away everything else about him.
It's already wacky when
Chief is standing around with a bunch of other Spartans and he's the only one wearing his helmet, it would've been so much worse trying to write around it in the show. You'd either have to make it an actual in-universe thing that he refuses to show his face, have him in full gear all the time even when it makes no sense, or make it into a joke where his face is always out of frame or hidden ("Halo: The Series," starring Wilson from "Home Improvement" and the the tall guy from "Police Squad!").
I think they made the right choice getting it out of the way early on the show. I even like how they leaned into it metafictionally, with using nudity versus armor as a symbol and metaphor, even though most of the audience just took it as "Lawl, buttz."
I mean, it's canon to itself, but it's explicitly set in a different version of the universe than everything else, called the Silver Timeline. It's kind of moot until we see the first tie-ins directly with the series, novels or comics or what-have-you set in the Silver Timeline instead of the game version, but it's definitely an official thing that there are two separate and distinct Halo continuities going on.