In Laravel 4, you could set an environment based config folder structure:
/config/app.php
/config/dev/app.php
/config/staging/app.php
/config/testing/app.php
Phpdotenv is about storing values in environment, not general purpose config library. Environment is UNIX concept and the values are always interpreted as character strings. Converting to different datatypes such as arrays or booleans even though convenient would be outside the scope of this class.
Laravel's config system is already separated. phpdotenv does environment, laravel does config. Then once config is done, environment is ignored. The concern of parsing environment variables from strings into whatever is passed on to laravel (weather that be their env function, or exploding inside your config files).
In other words, use Config::get() to get a specific conf file with your desired structure and you have what you need.
You should never use env() in the code directly when it is outside of the config folder according to the Laravel guidelines. It's a good practice to use config(). In config files use env() to get the data from .env file.