So I found a way to do this if anyone else runs into this.
Deployment hooks! -- love them.
I just added a deployment hook to create the symlink after the Install Composer Dependencies. The hook was this:
ln -s /home/forge/domain/.env {{release}}/.env.php
Switch out /home/forge/domain with whatever is the path to your project.
For the environment management in envoyer, I just put the php array code like this:
<?php return [
'FOO' => 'BAR',
];
So the .env file on your server has the php code and the .env.php file just points to it. Seems to be working fine. If there is a better way to do this let me know.