All your system-wide settings for your downloaded vagrant boxes are stored in .vagrant.d directory which is placed in your home directory.
.vagrant on the other hand is in you environment/project directory and holds individual projects settings i.e. your current VM settings. Whenever you create and execute a vagrantfile, a .vagrant directory is created with VM specific data.
The .vagrant.d/insecre_private_key is the default insecure private key to use your VM(s). It's replaced by vagrant on first VM start with private_key from project's .vagrant directory. In your example: private_key for default VM started with virtualbox provider.