Take the example recipe below:

{
  "type": "smelting",
  "ingredient": {
    "item": "minecraft:obsidian"
  },
  "result": "minecraft:bedrock",
  "experience": 10,
  "cookingtime": 20
}

You won't be able to shift click the obsidian into the furnace like ores and other vanilla smeltable items. Of course it was hardcoded on items like ores to be shift-clickable into furnaces. This trait does not get applied to items in this snapshot however.

EDIT

it actually doesn't require a custom recipe, regular vanilla smeltables are also not shift-clickable. + I discovered, after putting in the smeltable in the top slot, you can't shift click the fuel in the bottom slot, however, if the top slot is empty, you can shift click fuel in the bottom slot.