Currently, one does .gh-repo user/repo-name enable to turn on webhook notifications for user/repo-name in a new channel.
After this command, the plugin outputs a string of messages about setting up the webhook on GitHub, which are unnecessary when adding a repo that's already sending notifications to another channel connected to the same bot/plugin instance.
The webhook feature needs a fair bit of work at this point, but reexamining the webhook-adding flow should be part of that polishing-up.