That's the thing, it isn't nowhere as complex, and it can't be. First due to technological limitations, and second, it's a game.
And like you said, even with the current tech, we are limited. There might be a few reasons for this. I think the main reason is that they want the game to be available for everyone, meaning PCs/Laptops that are 10-15+ years old. Second reason is money. I don't think they could get near that level of customization with the current ME, and developing a new one will take a lot of effort, time and money. And it wouldn't be worth it in the end, because the requirements for the game would go up, meaning old computers wouldn't be able to run the game.
The current ME seems very rigid, and you can clearly see the "if x happens, do y". To me it seems like it takes a lot of effort to develop new roles, because then you have to program a lot of stuff from the scratch. You have to set what the AI will do and how they will react to certain movements. Giving that sort of freedom to a player seems impossible right now.
With your example, that stuff already happens under the hood...at least somewhat. Players that don't necessarily occupy certain areas will, to an extent, look to make runs into space, or cover empty spaces, depending on the roles, duties, instructions, etc. But often that's nowhere near enough to what you want them to do. They AI needs to be smarter, meaning doing all of these things, but better (being more aware of the space, better decisions on when and where to run, etc.).
Even giving some ability for the players to dictate those movements would be possible. Allowing to dictate how a role/player performs in certain phases of the play (the overall addition of In Possession, Out of Possession and In Transition was great, but I don't know why SI haven't expanded upon it more), meaning the buildup, mid third, final third, as well as in defensive transition and in offensive transition. Right now, you have "When team has the ball", "When player has the ball", "When opposition has the ball". Those should be expanded more, converting certain player traits to instructions, and overall revamping the whole PI screen just like they did with TIs.
Example: You have a double pivot. You'd want one player to act as a playmaker, dropping deeper to pick up the ball, while the other player will push forward. Now that's easily doable in the game right now. But, if you want to fine tune it a bit, it's where it becomes hard/impossible. I might want the player dropping deep, to drop right in the middle and occupy that space while our team has the ball. The player pushing forward should also push forward and occupy the central areas as a No.10 would. But instead you end up with something lopsided, where none of them really occupy the centre, but instead the side of the field they were positioned originally.
Another example would be the Inside forward/Inverted winger. What if I wanted them to defend wide, like in a 4-4-2, but then in possession they should be narrow and act as two No.10s (A lot of managers that use 4-2-4/4-4-2 do this). They will simply be too wide, until they get to the final third. Yes, you can make something similar to this in game, but it's never going to be exactly the same thing.
The hidden instructions (aka the hardcoded behaviors) absolutely do exist, but I'm not sure if we can 100% be sure of what they are. Those unofficial sources are probably true in most cases I'd say.