Q: The Meta Rule says these are played at the beginning of a game. Do you pull those out and deal separately?

A: You may notice that Meta-Rules have different backs from the rest of the cards. They are meant to not be shuffled into the deck at all, and the different back facilitates finding and pulling them if you accidentally shuffle them in. You just decide at the beginning of the game whether you want to play by those permanent rules or not. It’s like they are a house rule which all players decide on before starting.

This page has a short list and descriptions of all the MetaRules, with a little commentary.