[haneefmubarak]

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.