You can totally customize phpvms however you want. It is written in Laravel after all but it does look confusing at first glance because some files are renamed or removed.
All route definitions are written in RouteServiceProvider.php
TBH not sure why the author would remove routes folder.
If you are gonna add just one or two pages, I recommend you writing a module for it so that the logic you write is totally separated from the core phpvms logic. It'd make the code much easier to read and debug. Documentation for the module system can be found here.
If you want to rewrite the entire frontend, you may take a look at the template system that phpvms uses.
Good luck!
