... Unlike a building, though, the design of Moodle is ongoing......
I guess you hadn't been to our college parties. I feel sorry for some of the landowners. Their buildings had complete structural renovations.
Seriously, I guess my confusion comes/came in the actual design sequence of the module. For example, the journal module. When starting a new module entry, I see mod.php.
After setting up the entry, I get directed to view.php with an id number. This is where the main stuff the participant does. Then there is a choice to 'edit' which is the edit.php.
Finally, there is report.php where the instructor can review and comment on the journal.
As a non-programmer, it literally took me weeks to figure this out. The rest came 'easier' as a lot of the functions are like recipes and other references on php can be researched on the 'net.
I surmise that this is what happens throughout most of the other modules.