If there are billions of transistors in a CPU, there is no chance that somebody designed every single one of them manually. Is their layout calculated or something?
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Microelectronics engineer here.
Most chips (Or ICs Integrated Circuits) will have memory or storage on them. Each bit of storage is a repition of the same circuit. So on your Intel or AMD chip, huge parts of it are just copies of the same set of transistors, laid out the same way to form sram. The more benign parts of the circuit can use standard building blocks (think Lego with input and out holes for power and ground, input and output digital signals) so we can simplify the design.
The reality comes back to performance. The faster and more specialised the chip is, the higher the frequency is, then the more hand designed parts there are. We have tools that are very efficient at building parts of the chip, and there are some software libraries to accelerate this process. Languages like verilog and vhdl help, but often they form a starting point prior to hand optimisation of critical parts of chips.
Ultimately manufacturing chips is quite expensive, so unless you need the performance using more general chips and then writing software on them is going to save time and money. Hence why you mostly see Intel, amd and arm processors inside circuits. When the chips are custom, they often still have a general purpose arm processor at their heart.
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