With WCAs you can build audiences based on people who visited your site (or say, a specific URL like a blog post or a thank-you page). You can then use these both for retargeting (e.g. someone visited your site but didn't sign up yet), or build lookalike audiences out of website visitors and/or signups. Imagine that someone read an amazing blog post describing some key features or use cases of your product? Why not create a WCA and then craft a creative addressing that specific audience segment.
Another benefit of WCAs and lookalikes based on those is, that they're updated automatically, whereas for email-based custom audiences you'll either have to manually upload new signups to FB, or set up some custom automation to do that for you.