There is only so far you can go with cylinder head and piston design before you get to a point where you have a piston to valve clearance problem, or you have to short a cam duration to obtain the rpm to give the required power density.
There is a workable range of bore to stroke ratios for petrol engines and a different but overlapping workable range for diesel, taking into account required power density and therefore rpm, and consequences on valve size and number, airflow, piston speed, cam timing, compression ratio, forced or normally aspirated induction, injection nozzle or spark plug size and position.
I am sure I missed something.
Bottom line, like any design, there are complex multiple compromises and simple rules of thumb to try to quickly accommodate all the variables
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