Why there is a yaml file generated with the homestead box while there isn't one generated in a simple linux box like the precise64 box.
Vagrant itself only needs a Vagrantfile, Vagrantfile is a ruby script and as such can do many things. The issue is that it can come a bit complicate to read.
To separate the pure configuration settings, many people adopt external file (like yaml or json file) to store parameters that can be changed (like mapping folder, cpu, ram ...) and so the Vagrantfile will read from this external file.
The homestead project has adopt this way of working and it creates the Homestead.yaml file for you and this will be the only place you will go to manage your VM configuration