I realize this thread is older than dirt, but if those (admittedly few) of you who really want this feature are willing to invest a few hundred dollars for a fix, why not add some RAM and HDD space to your server and virtualize your server OS of choice to run hMS instances separately?
IMO, this is the cleanest way to get a completely different setup for each of your email domains... you'd have distinct (and succinct
) SPF records, DKIM pairs, and DMARC policies, as well as the ability to customize any of the various hMS included options to your heart's content. This assumes you have multiple public IP addresses, a router that you are capable of configuring properly for "One to One NAT" or similar, and sufficient hardware requirements (and physical access to the Host server for installation of RAM & HDDs) to run the various virtualized instances. If your server is part of a cloud based service, you could pay for another instance. Of course, this "easy solution" to your situation is the reason services like AWS offer (and justifiably charge for) those additional instances. OTOH, perhaps if the need is sufficiently high this will be a justification to move from shared hosting to CoLo or even a local server.
Done properly, this is a very cost effective solution to implement. I generally assume that one who has multiple IP addresses at their disposal already has a capable router, but in case you don't there are current offerings from the Cisco RV series starting at ~$65 US. If you don't have spare Windows Server licences for the VMs, you could certainly get the job done handily with any number of *nix variants which are open source. Virtualization Host could be VMWare ($$$), but I've used VirtualBox (also Open Source) in a production environment for a generally similar purpose with no issues whatsoever. So, really you're just looking at the cost of additional RAM and HDDs (and perhaps adding another physical CPU to the server in question if it has an open slot).
This solution directly addresses the OP, separating each domain to its own public IP, and doesn't really add much administrative or hardware overhead... especially when running *nix as the guest OS (as one could choose to install a VERY light distro or a trimmed down version of a bigger one with which the user has more familiarity / experience).
In my experience, paid solutions tend to be more user friendly, sometimes more flexible, etc. but if you'd like to accomplish the same goal with free solutions, you may have to jump through a few more hoops. YMMV
P.S. This is my first post on the hMS forums, so I must say I *really* appreciate the stable, high functioning, and FREE! hMS... it's been a lifesaver for me!