Magento2 Admin – How to Assign Simple Product to Configurable Product

I strongly recommend you to reconsider what you want to do as it creates conflicts on almost every aspect of Magento. Consider this:

1. Custom Options are meant for end user to "fine-tune" product. Predefining them in configurable product removes their main purpose. This argument alone hints that there must be an another way to do whatever you want to do.
2. Configured products have their own list of options. I don't think there's a simple way to build nested lists without rewriting pretty much everything from wish-list to credit memos. As an additional "bonus" update so extensive renders whole installation pretty much unupgradable.
3. Even if you manage to find workaround from this problem programmatically, there's no way to set custom options for simple products on the backend, making any product created this way a bag of hurt.
4. You can add Custom Options to configurable product themselves. This almost certainly creates its own set of issues.

It's much easier to generate a new simple product with appropriate attribute value and use that instead. And even if you need to integrate it with external inventory system, it's way easier to modify than rewriting better part of Magento.

There is currently an open issue on github.

Interestingly there seems to be other closed issues around this. At the moment i am not sure it is getting elevated to any degree. Maybe because people are not talking about it too much but it seems quite a fundamental problem when creating a configurable. Generating a product first before you get the option of manually adding other products is not a sensible work around.