If you register an email notification for multiple domains, you are notified for all domains.
However, if at some point you no longer wish to be notified about one of the domains, it does not seem possible to unsubscribe from one of the domains only. (If you unsubscribe from both, and then re-subscribe to just 1 of the domains, it seems like your previous multi-domain account with the same email is reactivated, and multiple domain notifications are again emailed.)