I was just informed that this functionality was added!!! 
You have to go into each of the metafields, and enable them to be used for collections, but after that, they will show up in the list! The only bummer is that the only option you have in the dropdown when setting up the automated collection, is “is equal to”. It is unfortunate that there aren’t options like, “is empty”, “is not empty”, or “is in” (to let you pick multiple values). We will find a workaround for those things though.
https://help.shopify.com/en/manual/metafields/automated-collections