Gerber Files

this is a complex question you have.

but this forum is about the altera tools and design needed just for the devices mounted on the pcb not a complete system.

maybe a different comparision.

you are using a pen to write something down on a paper, the pen is your tool like altera quartus, but it is not used to plant the trees and make paper out of it. thats a different process (and forum)

as you have a computer science degree then you know compilers, altera quartus is a compiler that makes out of some files describing the behavioral of a functionality some files that can be used to be downloaded into altera devices mounted on pcbs. or from a compiler point of view, same as like for example microsoft visual studio does it takes some source files and generates an executable file that runs on your pc. same for altera tools.

hope you understood and it has answered your questions.