There can't be clear cut rules for everything, so we have to make due with rules that don't cover everything. When a situation comes up that falls through one of the many cracks, the DM is going to have to make a ruling(say yes or no). I don't view one off decisions as Mother May I. Mother May I requires a great deal more consistency.
It's more about how often this will come up in a game. And how these these rulings are guided... what other elements are involved, and how are those elements determined?
So try to convince a stubborn noble NPC to assist you? Okay, the GM crafted the NPC, the GM decided he's stubborn and what impact that has, the GM decides the DC, the GM decides who else is around that may make things easier or harder, the GM decides if the player's Noble background impacts things at all.... and so on.
The more we throw into the bucket of "GM decides" the more the game leans toward Mother May I. Or is at least prone to problems that may arise from Mother May I, depending on how you want to define it.
And the only real situations that I can think of where a player is truly asking the DM, "Can I do this?" is when they want to step outside the rules for an exception. "Can I play a dragon?" "Is it okay if this prestige class(going back to 3e for this one) loses it's alignment restriction, because it fits my character so well?" "Can I sub this class ability for this one of the same level over there, because it fits my character better?" Those are all requests I have gotten in the past and truly are the player asking for permission to do something. But those are rare, so still not Mother May I.
Those are more character options being allowable or not. That's a related, but maybe separate issue... or a subcategory. The ones I feel are more impactful are the kinds of rulings needed routinely in play, and how to make such rulings.
Question for all, most examples we have seen of MMI is when the GM says no. If the GM says yes is it still MMI in your opinion?
I can see a case for it, yeah, though I don't quite agree 100%.
I've been focused more on MMI as a problem, but I think if a game ultimately works with "The GM decides" as the answer to "how is this determined?" then yeah. I think this is what
@Ovi's point was about the structure being one of MMI. I see the point because I mean, that's literally the way the game works in many ways. But I've been more focused on how that impacts play negatively.
Which as you suggest, is more obvious when the GM is frequently saying "No". It's less obvious when the GM is saying yes, and less problematic, too.
The reason I don't quite agree 100%, is that if we compare this with another approach to play, "Say yes, or roll the dice" as a principle, it's equally possible to always say yes. I mean, it's never going to happen if anyone wants to have any fun at all, but the distinction between these two approaches is the GM's ability to say "No" outright, so I think that's a key element.
But even in these cases the GM has final say. That's what things like rule zero are all about. And it need not be about what the GM has in mind (though it could be) it might also be to maintain fidelity with what has been established in the last five minutes of play, to fix a weird moment in the game where the mechanics feel like they pop out of place and aren't producing a sensical result, etc. With Charm the GM could always have you up against a monster he invented that is immune to charm effects. The GM might decide what you are trying to do with Charm exceeds the spirit of the description of charm. Or there may be some other interference in the setting that doesn't have codified mechanical effect but the GM thinks would interfere.
Here's the thing.... invocation of Rule Zero only affirms that the game is Mother May I. If we place the GM above even established and clear rules that (under normal circumstances) we can all agree upon, then that's making the game Mother May I.
Barring such rule zero use, the game works in certain ways. If I roll a 14 and the monster I'm attacking as a 22 AC, I've not missed due to Mother May I. I missed because the rules and the dice said I missed. If we accept that the GM can, at whim, overrule these play processes, then yes, we're saying these rules are at all times subject to GM approval, and that absolutely makes the game Mother May I.
As for certain setting elements like your immunity to charm example, I think it depends on how such things are decided. More old school play, this would be something predetermined by the GM and would be an element of the challenge in place... here's a creature they can't charm, how will they deal with this? I think for the most part, 5E assumes this approach.
But if a GM just decided during play, "I was looking forward to this fight, I'll just make this thing immune to charm" I don't think we'd see it the same way. But rule zero type thinking says that this is fine.
This is why I don't think we should ever take the rule zero type of caveats as expectations. They're not meant to support crappy GMing or bad decisions, or the GM maintaining their prep over some curve the players have taken. They're meant to deal with edge cases that the rules don't really allow for.