How to install Commerce 2 on Drupal VM?
Like the Commerce docs say, you need to install it like any other Drupal 8 site. So, it is easier to use the composer command. 

composer create-project drupalcommerce/project-base MYNEWSITE --stability dev

Where MYNEWSITE is the new Drupal 8 w Commerce 2 directory. You can do this anywhere on the host machine (ex. I always have them in /Sites).

From here, you can add Drupal VM to the project and tailor the config.yml to your needs, then vagrant up - just like you did with the vanilla Drupal 8 site you already installed. You should see the Commerce install screen.

There is likely a way to automate this with DrupalVM, though I have not tried that approach.