I again turn to my "degenerative disease (such as cancer) is a dysfunction of cellular machinery" analogy. Cancer is what happens when cells cease to follow the "I'm part of a multicellular life form" model and instead begin to realign toward an "I'm a single-celled life form" model.
Certain people will have a high personal risk of developing cancer (e.g., those who have a family history of certain cancers), while others will have a low risk. Certain materials (foods, additives, consumables like cigarettes, construction materials like asbestos) have a quotient of cancer-liability, which we usually call "being w cercinogen." I want to stress that they don't contain cancer, cancer can ONLY occur in living cells.
Etc. I doubt I need to spell out the whole argument here. The fact that people don't randomly eat food or smoke or fly in airplanes (social and familial patterns exist) doesn't diminish the fact that tobacco smoke or continuously going to get a tan massively increases your risk of cancer, to the point of "it's less if and more when." The fact that some folks have a naturally lower risk of developing cancer is irrelevant to whether compounds can be carcinogenic. It matters for whether an individual person will develop cancer, which is of vital importance for managing health especially as we age. The fact that some folks can expose themselves to all sorts of carcinogens and die of "old age" rather than developing cancer is similarly irrelevant to whether substances or activities can be carcinogenic. It would be foolish in the extreme to conclude from these facts that diet, activities, and environment can be neglected.
Some rules have extremely high risk for MMI, but have or develop strong protection against these concerns. Some of these protections are formal and enforced, albeit not part of the mechanics themselves, analogous to nurses limiting the amount of X-ray exposure someone experiences as a result of medical examinations. Some of them are informal but highly recommend, analogous making sure to put on sunscreen if you're going to be out in the summer sun for an extended period and wearing a good hat that can protect your scalp. And some are a lot fuzzier and dependent on people being vigilant about small details that can easily be missed, analogous to being really careful about one's diet or the like. Finally, some may be entirely tacit and presumed, like smoking being generally understood to be bad for the smoker now (to the point that it is now used as a trope to indicate that a character does not care about their safety or well-being.)
Meanwhile, other systems are less susceptible to MMI because of their design. MMI depends on faults in communication (usually centered on deficient understanding of expectations, as you noted), sustained concentration of authority in a single specific participant, and an inability to address or correct issues other than by interrogating that authority. There may be other factors, but those seem to be the salient ones. This, a system which explicitly requires steps that contradict these things will avert or even eliminate MMI. If communication is heavily required simply to play the game, you will already cut off a lot of these risks. If authority is explicitly shared, then you forestall anyone becoming a "mother" in the first place; this sharing does not need to be symmetrical either, it just needs to be sufficiently complementary such that each participant has agency and a clear part to play in the process. If the game provides pre-defined structures and options which enable the lower authority participants ("players") to deal with and respond to issues without having to always jump through invisible hoops, then the "may I" side is curtailed, e.g. things like the X-card for meta level issues and things like spells or powers for IC situations. These rules design elements are separate from, but work in tandem with, the aforementioned policies, procedures, etc. that a game can develop to defend itself against this type of dysfunction.
I find that 5e does little to nothing of any of these actually-in-the-rules defenses against MMI, and in fact tends to go out of its way to avoid or undercut them. It encourages DMs to avoid direct communication, to conceal things and play fast and loose with what has been communicated. The game absolutely pushes the DM as the central and all-encompassing authority, with little to no cyclic exchange of authority and a strong emphasis on "you ask me, then I tell you" DMing. Other than spellcasting, which as in pre-4e editions is essentially the one bastion of respected player influence, everything is left so deeply in "ask your DM" territory that the rules themselves are reduced to suggestions.
Further, I find that of the non-mechanical policies, procedures, etc. that are meant to mitigate these issues, none of them are of the first two types. There are no formal steps for addressing these concerns outside of the rules, and at best minimal informal but highly recommended steps. Instead, it relies almost entirely on DM vigilance, players being willing to speak out, and the presumption that if something goes wrong, the DM will fix it.
That, to my mind, is exactly the recipe for a game to be rife with MMI problems. Both game design and game policy have had every formal, shared, open structure for addressing this issue removed or downplayed as much as humanly possible, leaving only soft-touch options, implications and social contract stuff, which is really, really easy to screw up or forget about or go overboard with.
And, as a result, I now have a better response for something mentioned upthread.
My problem is, as I have only now realized, these DMs are putting the cart before the horse. They have confused cause and effect.
The fundamental underlying cause is, as they have noted, the hyperdependence on DMs to fix everything, everywhere, all at once, to be the clearinghouse, to adjudicate everything all the time. Initially, this led to a resurgence of what I'll call "Lite Viking Hat" DMing, in that it's still a dictatorship of the DM, but it was viewed as a liberation from stifling confinement "so things can finally get done," as it were, rather than the declaration of martial law. But all too quickly, this led to poor behavior on the part of DMs, and unfortunately, the old-timers collectively provided no help on this front. As this person notes (and as I have highlighted many times), the DM side of the culture of play was radically unhelpful; every rules-question thread would almost instantly get a ("We can't help you, ask your DM"/)"I am the DM and want help"/"You're the DM! Just do whatever you like!" interaction. This repeatedly reinforced on a cultural level that the DM should do whatever they like, whenever they like, for as long as they like.
This hit a problem when D&D started growing a fanbase much, much larger than the old one. Because the new players are not conditioned to meekly defer. They have no reason to; if they wanted to meekly defer to ironclad determinations, they could go play WoW or FFXIV or Elden Ring or whatever else. So they advocate for themselves. They talk back. When they're pushed, they lay down requests, and they do get upset when their requests are ignored or overruled, and they cry foul at the level of social contract and interpersonal respect. They have to. There is no other level to which they can appeal; the rules are but suggestions, the culture of play is DM power über alles, and the principles (and other policies/procedures) have been intentionally gutted of any formal content that can be drawn upon or referenced.
The fans of the oldest school stuff have gotten exactly what they asked for. You only have conversation between adults as the solution to any problem. The DM is the absolute, unquestioned and unquestionable, universal, unilateral authority, with the game being but her plaything to use or break as she sees fit. All game function exists solely on and by her will. And now a number of people are finding that no, players-in-general are not particularly happy with that state of affairs. Worse, when things go wrong, to their shock and horror, the consequences fall upon the person with all the power, the DM.
