Immersion-breaking? What about play-ability? The civ's that depend on wood - depends on the map. If no one on your team can trade that resource... You are SOL.
It's just a 'different type of wood'. It's like having a civ that can only gather pine, trading it for oak. I get the need for immersion. I just think playablity is better and more important.
Also with separate resources, it'd be better for Hyrule to team up with the Gerudo than the Zora's. That break's immersion. You'd basically be crippling yourself to join a team with anyone that doesn't have or can't trade the resources. Besides, when you're playing the game and immersed, you're not trying to figure out what resources your ally has. That is more meta-immersion which I don't think exists. You are immersed in your city, not your allies bank.