The feature size is 7nm. That's like saying the tightest radius in your CNC mill's tooling is 3mm. The stuff you make is far larger. Just look at the SRAM area: it's .0269 square microns. And SRAMs are tiny compared to "gate" RAMs, like you'd see in a book.
17 million gates per square millimeter.
The smallest logic I've heard of is a transistor using 7 atoms in toto. That is a factor of 70,000x, or about 16 generations.
Now, how we'll get there, I don't know. Also, I think the generation gap will probably widen to 5, or more, years. So... 75 to 100 years of "room"?
We can see the end of the road. AFAIK no one has any clue how to even start thinking about 2nm or beyond. No one is even certain we will hit 5nm.
https://en.wikibooks.org/wiki/Cell_Biology/Introduction/Cell...
But you're right, actual stacked chips ("3D" ICs) aren't used much, largely for thermal management reasons.
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.