While the hub is great - assuming a one to one relationship of domain names to websites, is a little misguided. A better approach would be to allow for a site to have multiple domain names and link them. Also, allowing for one of these to be set as the primary domain name would allow for those cases where only one environment can be patched.
I would propose that you:
Allow for grouping of websites in your hub (ideally during the login process inside wordpress).
Allow for the selection of one of the "site URLs" to be marked as the "Live" site for display purposes, alerts, backup, etc..
While it would be great to be able to flag a site as "able to install" updates/plugins, the reality is that if you offer the above grouping, and display the details of the "Live" site for the group Developers will know which of the sites in the group are able to have patches installed. In some cases, it may be directly to the live sites, in other cases (like ours) only certain environments are even writable. The grouping and display based on the site marked "live" solves for both of these issues, reduces clutter in the interface for organizations that manage several environments for site development, and allows for some utility that is currently possible.