I have a 1.9.8 instance and a 1.12.
I believe you are correct - this rule matching only picks up the initial description, and not the follow up Internal notes. I'm working on similar..
My Goal: I would like our internal users be able to reply to an alert email, and have that reply be filterable.
For example, if Employee A gets a Ticket Assignment Alert email, I'd like her to be able to reply to that email "give this to #chris" - reassigning the ticket via filter without having to log into osTicket.
Sorry for the partial thread hijack; looks like you were looking for similar albeit five years ago. I'm still digging for a solution.