This annoyed me a bit but it's not a big deal. You make two skeleton templates: One for full documents, one that has nothing in it except the parts that change

This annoyed me a bit but it's not a big deal. You make two skeleton templates: One for full documents, one that has nothing in it except the parts that change (say, the meta > title, the body > main and the body > header > nav parts) each wrapped in a hx-swap-oob. In general, out of band swaps are really, really convenient for non-hierarchical layout relationships.