Out of Office comments when a customer answers to an absent JSM agent
Currently, the Out Of Office Assistant doesn't publish an Out of Office comment when a customer replies to a request that is assigned to an agent with an active rule. However, you can create a workaround to reassign the request to the same assignee, thereby triggering the comment.
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Building the Automation
In Jira hit double g and search for "Automation Rules". Then add a rule like the following to each Service Management project where you want it to be active.
Every time a comment arrives in an issue and the assignee is out of office, it will reassign it to himself and so trigger his out of office rule.

Step 1: Trigger with an issue comment
Go to triggers, and select: Issue is commented
Step 2: Evaluate whether the assignee is Out of Office
Select a condition: JQL issues present
Set the following JQL: assignee.outofoffice.today=1
Step 3: Exclude the author's comment from the automation
Select a condition: JQL issues present
Set the following JQL: assignee != {{issue.comments.last.author.name}}
Step 4: Create Smart Variable
Select the Action: Create variable
Select the Variable name: currentAssignee
Enter the smart value: {{assignee.accountId}}
Step 5: Unassign the issue
Pick an action: Assign the issue to
Select Unassigned as the assignee
Step 6: Re-fetch data
Add the action: Re-fetch issue data
Step 7: Assign the issue to the original user
Add the action: Assign issue
Set the smart variable {{currentAssignee}}