Ok! Our media agency asked Google and got the following answer:
_My understanding is that your main goal is to be able to import those Google Analytics goals into AdWords, and yes you would need to use Autotagging for this. If you're already using manual tags, which it sounds like you're doing through core-metrics, you can still use Autotagging and Google Analytics will ignore those manual tags as long as they aren't Google tag parameters such as Campaign Source _