Though, I have another suggestion.
In our setup we have disabled the standard notifications sent out by JSD. Instead we are using JIRA Enterprise Mail Handler (https://marketplace.atlassian.com/plugins/com.javahollic.jira.jemh-ui/versions#b100702500).
You can then have full freedom to customize all content of the email sent out to you customers; add logo, include custom fields etc.
Hmm, unfortunately that's a showstopper for our part. It's a shame to see such a great product as Jira Service Desk falling short on basic functionality that is needed to make it an alternative to Zendesk and similar.
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