Will the order display the SKU Number you input for the Custom Options? What if there is 4 different Custom Options to choose from, and each Custom Option has a individual SKU, how will that work?
SKU is only for products.
It should be unique.
But products are not identified by SKU, they have unique ID. You can see it by $_product->getId();
However you can filter product or fetch any particular product by its SKU by,
Hope it helps you