Runes can be put into the inventory crafting (and possibly other custom items)

There are restrictions on putting runes into a regular crafting table, but no restriction on putting runes into the 2x2 crafting table in your inventory. This means that, for example, you can craft a book with 3 runes + 1 leather (lol). Unsure if this also applies to other custom items (Sell chests, etc)