Service Desk email format/links on issues created from email vs. customer portal

(This is a cross-post from https://answers.atlassian.com/questions/229837/service-desk-email-format-links-on-issues-created-from-email-vs-customer-portal as I was advised to report this as a bug here based on the response by Brad Baker at Atlassian.)

In trying to create a consistent customer experience for our end-users who we're now supporting with Service Desk, I've noticed that emails sent by JIRA for issues created by the Email Handler use a different format than emails sent by JIRA for issues created via the Service Desk Customer Portal.

Example #1: Email format for issue created by Email Handler:
https://dl.dropboxusercontent.com/u/16273/Screenshots/email%20from%20issue%20creation%20via%20email.jpg

Example #2: Email format for issue created by the Service Desk Customer Portal:
https://dl.dropboxusercontent.com/u/16273/Screenshots/email%20from%20issue%20creation%20via%20customer%20portal.jpg

I'm looking for how we can setup the email handler in Example #1 to match the email format (including links to the Service Desk Customer Portal) in Example #2. Right now, the customer experience is like we're using two separate systems for this. Links in Example #1 go to the default JIRA UI instead of going to the Service Desk UI for customers.

It's like we need the ability to create an email handler for a Service Desk – but I see no way to do this in OnDemand. Is this working as designed or is there a bug with the code that Brad says "tries to suppress the fact that the reporter gets both a SD email and a JIRA email?"

As an additional note, issues created in JIRA via email handlers do NOT show up under the "My Requests" view from the customer portal in Service Desk. It's like our email handler is ignoring the fact that we have Service Desk enabled. I wanted to mention that here in case the two issues are related, however I can submit a separate bug report for this particular problem if need be. FWIW, we were a Service Desk Beta user in case that has any implications on our configuration.

Our SEN # is: SEN-2196722

Thanks,

-Eric