I think the confusion is coming Agile's statement that you need to switch from the Mac OS keychain to the Agile Keychain in 2.0 before upgrading to 3.0.
Originally, 1password stored its information using the built-in Mac OS keychains. Eventually, they decided this was limiting them, and decided to create their own "Agile keychain" format. 1password started using the Agile Keychain a while ago, but it was necessary for existing users to upgrade the Mac OS keychain storing their data to the an Agile keychain. If you're an existing 1password user, this must be done before you upgrade, or else (apparently) bad things will happen.
However, if you're not an existing 1password user and you're just using the Mac OS keychain to store your passwords through Safari, you can just start with 1password 3. It'll use the Agile keychain format by default, and is able to import your passwords from Safari.