I totally agree, I ran into this too and haven't been sure of which way I'd like to solve it. For now I've added iron and copper plate sink recipes. I THINK with some smart buffer management and priority splitter use you should be able to have the machines working and capitalize on the original scrap processing recipe. Even if the cubes are all sank into plates it should still be more advantageous to do so over smelting raw ore.
I will keep thinking on the recipes and see if improvements can be made while keeping it an interesting puzzle to solve.