The mismatch was supposed to be fixed when the retail-version uses the updated FoC RAM patch, but i've not seen any confirmation that this is actually the case.
I can confirm that it works. Though, it would seem that due to some unknown reasons that it will most likely not work unless you install the patch on a freshly installed copy of the game. And, I have a friend that told me it would seem that mods break it, though he was using Republic at War, which installs patches to the game itself (apparently, that is what he told me, idk) but me and some other friends are in the process of trying out Imperial Civil War in mulitplayer - me and another are on Steam, the other is on Retail. Will get back to you guys on whether or not Imperial Civil War breaks the compatibility.