This might be your point (didn't quite get your point) but that's exactly why you should fix this. You actually have separate inbound and outbound channels. It's rediciously simple to change those outbound channels' email addresses so that a direct reply will be sent to the corresponding inbound channel. It doesn't matter if the system is basic and uses a smtp server or if it uses a hot new email routing service. It's about setting the correct from address in your systems code.