Ok, a few weeks ago, I setup a 2008 R2 server, just for kicks, on an old Server. I'm using a trial license. I had installed Kabuto, and enabled anti-virus from the web portal. Emsisoft installed, but doesn't take the bundled license key. I did some checking on my own, and it seems that the same install program is used whether it is installed on a workstation or on a server. The platform check (probably just checks the OS type, but I digress), seems to happen when Emsisoft is run, rather than when you install it.
Long story short, without a antivirus server edition license key, I can't test 100%, but I would imagine it would still function as expected if you manage your own license key. The only potential bump I can think of, is IF Kabuto tries to verify the custom license key on it's own, but doesn't "know" about server keys.
I'll leave the rest to the professionals.
--Aaron