MMI is more of a GM issue than a rules issue. It varies from GM to GM as to how big of an issue it is, but you cannot codify everything that is going to happen in an RPG game. Attempting to do so simply results in an overly complex set of rules that ends up with you spending more time looking up esoteric situations in an oversized rulebook than just saying yes and moving on.
Just last night in my weekly game (Pathfinder) we were playing gridless. My character likes to get flanking and several times I asked the GM if I could get into flanking. There was no arguing about it or debating it, he simply said yes and we moved on. Had he said no at some point I would have been fine with that as well as we trust each other.
I agree that the impact of MMI-rules depend on the group. Especially in groups that have played together for a long time, there is an understanding between players and DM that often allows players to predict how the DM will rule and moreover there is a sufficient level of trust that rulings will typically be fair.
However, in less then ideal situations, misunderstandings between players and GMs can often result in bad experiences or at least in a lot of extra work for the player, if the rules system does little or nothing to support the decisions the GM makes.