Not seeing the country list in the database nor any settings around them.
I'm writing a custom shipping methods module and need to convert the three character country code into the two character code.
What is the best way to get the list of countries for use server side?
Unfortunately VC does not contains countries resources for using from server side code. But I would to suggest for you to include this countries JSON from our storefront GitHub repository as embedded resource into your module project and read it as described here.