I don't think that's quite right. We only have to worry about emergent behavior precisely because running a full simulation is intractable. If we could "just" run full QM instead of MD with all those lossy force field approximations all the emergent behavior would happen on its own. But obviously doing that is well past science fiction and into the territory of wild fantasy.

I think misconceptions commonly arise because there are so many examples where we know how to simulate each part with arbitrary precision but the scale of the system is where it all falls over. That just doesn't match up with our everyday experiences because systems on the scale of avagadros number or O(n^7) algorithms applied to absurdly small timesteps are anything but typical. It's difficult for people to wrap their minds around the implications of having to consider things on nanosecond timescales.