A computer does not “arrange transistors”. They aren’t moved around to form circuits to run programs, they already are in the required configuration within the CPU. The CPU is manufactured that way with everything already in place as needed.
Computer programs simply interact with the CPU as it is designed to perform their tasks. It is a matter of writing the program in such a way as to interact with the CPU in a desired way, and for that the size of the transistors is irrelevant.
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