When upgrading to high level machines you often use a lot of resources on top of what as already been used yet the machine stays the same size. For example, making the original machine with a machine block and then upgrading it with an advanced machine block.
My suggestion would be for a craftable bench that would go next to your crafting bench and whenever you upgrade machines there is a chance for dust (of whatever metal being used) to accumulate from the process of crafting said machine.