Product Customizer does not touch your existing variants. You can mix and match product variants and Product Customizer customizations if you'd like.
This is especially useful for when you need certain options for your product to have different SKUs, but not others. For example, if you need your T-Shirt product to have a different SKU for each size but not for each color, you could create Shopify variants for the sizes, and use Product Customizer to specify the colors.
You can see samples of this in action in our demo store.