The structure is good. You can read what's happening clearly. It also shows what's a laravel idiom and what is modern php. I giggled a bit when reading the user factory code. It feels so enterprise. Not a bad thing in itself. I was just happy to see php code that is not a ball of mud held together by holy water. :)
I don't know. If something is defined as "lightweight" (their word, but same point applies to "minimalist"), I should not have to blow my entire brain memory stack keeping the filesystem structure in my head just to start to examine how it's done.