I just saw that there is a duplicated issue on this matter: Issue - Github Webhook Branch Specific
Would be cool to have this solved in the near future as these deploy tasks are really helpful! :-)
I am seeing the exact same issue. I created a page and a subdomain (production and staging) and created there two git repositories (twice the same repository). This gives me two webhook URLs which I added both in the repository.
When configuring the git repository, I selected "Automatic...