Is my amended return covered by the audit defense I paid for on the original return?

Yes. According to the audit defense terms of service, "Audit Defense means that TaxAudit will represent you through the completion of any income tax audit for the tax return year identified on the membership certificate during the Period of Membership. Since your amended tax return is the same tax year as the original return and that tax year is identified on the membership certificate, it is covered. 

https://turbotax.intuit.com/corp/auditdefense.jsp