It takes years just to figure out how to use the machines to produce actual working chips. They're the most specialized, intricate, expensive machines in the world. They're operated in enormous clean rooms that only allow for 1 half-micron sized particle per cubic foot. No fab is going to run them without exactly following the procedures they have spent billions developing and testing. They are also going to avoid potential delays as much as possible because these machines have to be running for as much of their useful life as possible to recoup the vast expense. The level of risk-averseness is insane, but warranted.

If you haven't watched this video, I highly recommend it: Indistinguishable From Magic: Manufacturing Modern Computer Chips https://www.youtube.com/watch?v=NGFhc8R_uO4 It's a little outdated now, but very comprehensive and gives you an idea of how totally nuts the chip business is.

Think of it less like moving transistors around and more like moving small groups of atoms around (also, you can get single transistor cells for analog and power designs). The processes required to place the rough groups of atoms in roughly specific places involves extreme amounts of energy relative to the size of what you are working with, which is supplied in a combination of chemical, radiation, and thermal forms. As a result, predicting what additional effects attempting to form specific micro-shapes might have is nontrivial. They extensively simulate and then carefully test all of their approved cells on an ongoing basis. Deviating from this could cause unknown issues, including damage, but doing the necessary work to prequalify your custom cells would be prohibitively expensive for most applications.

NB: this is obviously a simplified explanation.

Going outside of the PDK rules you risk contamination because a chip machine is a high speed ultra-accurate automated mechanical and chemical laboratory. It sprays extremely corrosive acids and vaporizes metals. Going a nanometer outside of the rules would send droplet or flakes of chemicals flying around at high speed.

https://www.epfl.ch/research/facilities/cmi/equipment/photol...

It wouldn't, except potentially for macro-level requirements like maintaining the correct fill ratio [1]. Sibling comments are FUD.

1: https://semiengineering.com/knowledge_centers/materials/fill...

I'm very skeptical of this too. I don't see a mechanism where moving transistors could break the machine. Although I wonder if you could blow up the die testing machine by making a chip that was one big charge pump :-)