sudo just gives you temporary root permissions. You can think of the sudo command as a temporary switch user command. The su command in linux allows you to switch user so sudo is like "switch user, do as". Try it yourself, with your main account type the whoami command and it should return your username. Then type sudo whoami and and it should return root. This just tells you that what ever command you run after sudo you run with root permissions.
RE: How to properly setup SSH Key Authentication - If you are logging into your server with root, you are doing it wrong!