Levels of abstraction. I agree that there should be more exposure to the roiling dynamics of it all. From the high-fidelity simulations I've seen, you should think of a large macromolecule more as a tumbleweed or raft of seaweed that is being bombarded by water than as something made out of rigid pieces.
Yup. My school-acquired view of cells was always of somewhat squishy, mostly empty structures. It wasn't until recently that I learned they're all densely packed bags of molecules, shaking like crazy, and in which a lot of functionality depends on random walk making everything eventually bump into everything else.
