You have to keep in mind that the system is ABSTRACT. In order to have a usable ship construction system the designers needed a "costing" system, and usually the first thing that springs to mind is the system size VS available space system. That way it forces you to put some thinking into the designs you're doing. A size 4 escort can't have it all: very durable system, 12 torpedo launchers, fast engines, etc. It forces you to make choices and in the end you get more balanced designs, which after all is more "realistic". That being said in terms of "real-world" engineering you are absolutely right.
"No captain kicked ass, took names, outsmarted the machines, and then scored the babes like the Kirkmeister" -Liquidator Queeg