There are additional factors that make molecules in cells not subject to pure diffusion rules. Charge depending on the pH of the area ( even if in such a crowded space it is likely not really a pH anymore), and molecular interactions. Proteins (and virtually any other molecules but proteins and to a lesser extent nucleic acids are particularly good at that) can stick or be repulsed by their overall composition (external charges, hydrophobicity) but they can also stick to each other. Biology is fascinating but you can't isolate it long from chemistry and physics if you want to understand it.
Yeah see the art of David Goodsell. I believe he said the concentrations of the various biomolecules are roughly accurate based on calculations he does before starting painting. Cells are incredibly crowded. The human body being 60-70% water is usually presented in pop-sci as “wow we are mostly water!” but that’s actually very concentrated for chemical reactions. You usually don’t perform reactions that concentrated in a lab whether it’s biochemistry, organic chemistry, inorganic, analytical, etc. It’s a wonder all this stuff doesn’t just gunk up and precipitate out of solution.
All the living cells spend continuously a lot of energy as long as they are still alive for avoiding the appearance of precipitates inside the cell, e.g. by pumping out of the cells the ions of calcium and sodium and pumping inside the cell the ions of magnesium and potassium, because the former are much more prone to produce precipitates than the latter.
This continuous ion pumping is a major component of the energy consumption of a living being when it is idle, apparently doing nothing.
It is a big part of the communication, regulation and sensory system of cells. A lot of receptors are linked to ion channels for example. That's also the reason why there are pumps to bring the ions back on the other side too.
All these functions have appeared much later, most of them only in multicellular living beings, billions of years after the appearance of the living cells, and they have just adapted the already existing ionic pumps to other purposes.
In the beginning, ionic pumps had only 2 purposes, both essential for the survival of any cell, the first was expelling the ions that can form precipitates and the intake of the useful ions that are not dangerous, and the second was the energy interconversion between ionic gradients and forms of chemical energy like ATP hydrolysis/condensation.
