When you create a bundle with the product kits app, it does not create any separate product in Shopify.
The Product Kits app allows you to select an existing Shopify product and assign the child products to it. Since the product used to create the bundle is a Shopify product, it is displayed and can be customized like normal Shopify products. All the customizations, apps and add ons can be added to the product without any hassle.