Individual products do not have to be made available outside a bundle to feature as part of a bundle. These individual bundle component products can be unavailable.
Bundle Builder doesn't specifically check their availability. This means you can have products inside your bundles that are otherwise not for sale on your site. Alternatively, you can have products active in your bundles and also elsewhere in your store.
This applies for both bundle types; customers can order unavailable products in both the Multiple SKU and Single SKU bundles.
You can achieve this by going to Products within your Shopify admin space, and disabling online store channel availability. This will leave the product available for Bundle Builder to use, but will no longer appear in your collections or search results.