The extension detects a protected domain and saves the password, when the user logs in for the first time. For each protected domain, it saves its own password.
If all the protected domains have the same password, they can put only one of them in the protected domain list. The rest of them can be excluded, assuming you trust these sites. This way the extension will save only one password that the customer can easily update.
When browsing to sites that are excluded, the extension will not alert for password reuse. This is because the extension is not looking for password reuse in excluded sites.