Use webform submission id in custom content type
You're right - you can't use references with the webform submissions, because webform submissions are stored in their own special way - they're not actually proper Drupal entities, so they are not properly exposed to other modules expecting to interact with entities.

One thing you can try if you're not too far along in your project is to use the alternative Entityform project.  That should expose form submissions to be referenced.

Let us know if it works!  I haven't used the module myself, I've just heard of it.