I understand and agree, but most biological components at a sub-cell scale are membranes and pores in membranes, or even linear or circular structures like RNA/DNA.
Proteins are indeed incredible little machines and for someone with a computer background, they are the most interesting entities in the biological zoo. And proteins may be very large, some are hundreds of nm.
But by seing proteins as components, one misses the transport and signaling aspects which are important inside and outside the cell. It is a problem of scale, if we focus at some scale level, we miss what is going on at a smaller as well at a larger level. I think there is no easy solution to that problem.
But you're right, actual stacked chips ("3D" ICs) aren't used much, largely for thermal management reasons.