I am not sure if you are still looking for the answer, but you can set the Reply-To header using the API.
h:Reply-To
I have been using it with an email hash - each user gets a unique hash in the reply-to field so I know who is replying. Basically the reply-to looks like this:
"h:Reply-To" : "inboundaddress+hash@mydomain.com"
In the routes panel add the following and you can redirect to your email or to an HTTP endpoint:
match_recipient("^inboundaddress\+(.*)@mydomain.com")
Hope that helps. Justin