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.
In contrast to other projects such as YOURLS, Polr tries to be minimalist by avoiding heavy graphs or unnecessary bloat.