I don't disagree that restrictions on player choices can be useful. I want to start off by saying that.
And I know a lot of this has to do with the nature of online discussion. I've never really experienced such strong clashes of this type at the table. Typically, when this kind of thing comes up, we work it out amicably. The player either changes their mind, or the GM changes things a bit to accommodate the player request.
What I struggle with is the idea of theme, as it's used in these discussion. Or "vision" as it pertains to the game world. I genuinely believe that there can and have been compelling reasons for restricting player choices in games. But I also believe that there are plenty that are more capricious, but are kind of disguised as "setting integrity".
I very rarely feel like the restriction is justified.
Again, I'm not saying it can't be. We can all imagine a world where the gods have moved on, and there is no more divine magic. The world is more gritty and harsh, and there are no clerics. Okay, got it. Setting aside any concerns for if the game can still function with such a change, I can understand the theme and the story elements that went into that decision. Someone pushing to play a cleric in such a setting would be a bit annoying, and the player should work with the DM to come up with something else.
In most cases, though, I don't know if I agree that the justification really works. I have two examples, one that comes up a lot in these talks, and another that I recently experienced.
Dark Sun and gnomes. So you sit down to play Dark Sun and one of the players, for some inexplicable reason, has made or wants to make a gnome. Per the setting lore, the gnomes were wiped out, so the DM is leery of allowing the gnome. But really, why? Who cares if it contradicts the lore? We make our own lore. Okay, maybe it's a long standing Dark Sun game and there has been no mention of gnomes before now. Again, so what? Athas is a huge place. The gnome can be a wanderer from some other area where a small tribe remains, or whatever other idea may work. The gnome PC does not mean that hundreds of gnomes have to show up all of a sudden. Maybe it can be a focus for that PC, or maybe it won't matter at all. Dark Sun has all kinds of mutated creatures, so it's insanely easy to justify the gnome. And as I've said before, if one gnome can upset the theme of your Dark Sun campaign, then you're likely not focusing on the themes that actually make Dark Sun compelling.
There's really no compelling reason to block gnomes from Dark Sun. And I say that as someone who really doesn't care about gnomes or even get what they bring to the game.
The second example came up recently in a game of Star Trek Adventures that my group played. We have one member of the group that is a huge Star Trek fan. We have two others who are also big fans, and then three that are moderate fans (including me). So the GM decided that the game would be set in The Next Generation era. One of the players who is a casual Star Trek fan wanted to make a Klingon character. The GM restricted that race because "there was only one Klingon Starfleet member at that time, and it was Worf". So the player wound up making another character. There was no big dustup or argument about it....but this struck me as really odd. The GM's sense of fidelity to the setting trumped the player's desire. Basically, the GM decided to maintain the unique nature of a NPC rather than allow the player to play what he wanted. As if having a second Klingon in Starfleet would somehow "ruin" the setting.
To me, this is a clear case where it's basically let the player play what they'd like. The justification to maintain the setting status quo as it relates to Worf seems a very odd decision to me. Who cares about Worf? He never even showed up in our game at all.
So all this is to say that although I think there can be good reasons for restricting player choice for races, classes, or whatever other options there may be.....I don't think all reasons are good. I think there are some bad reasons, or meaningless reasons, more often than good ones.