I am publishing to my own "custom" domain. It would be nice if I could remove the option to publish to the webflow.io domain from the designer. I'm afraid I might accidentally publish to the webflow.io domain one day and get penalized for duplicate content.
You can remove publishing to subdomain when you have added a custom domain.
Even if you continue to use the subdomain for testing purposes, you can avoid duplicate content by going to Site Settings > SEO > Disable Webflow Subdomain Indexing. Select that option.
This has already been discussed here