For the create issue or comment mail handler feature, it would be nice to extend it such that certain automatic or custom replies to the email sender can be configured

A scenario in which this can be very useful is where JIRA has been configured in the workflow step properties (using jira.permission.comment) not to add comments (including via email handler to closed issues). In this case it would be useful for users who send emails to this closed issue (send emails having the issue-key in its subject field) to receive an automatic notification that their comment couldn't be created because the issue is closed.