The fact that steam installed modules can connect with non-steam installed modules via a server for online sessions is great and I applaud ED for making that possible.... That in itself really solves most of the issues in my mind.
However, from what I've read here and elsewhere, the compatibility issue seems to revolve around two different DRM security features, namely Starforce and Valve. It seems to me that it would benefit ED much more to totally convert to Valves system of DRM checking than sticking with "Starforce"... I mean who are "Starforce"? Does Starforce provide you with a vast customer base to promote your product together with a very user friendly system to update and manage all your applications?
If ED converted to the Valve system and drop the Starforce DRM system then ED could still sell their products via their online store as well as the steam store as not everyone likes steam, but the big selling point would be that the module keys from ED Store would be compatible with the same Steam store DCS module; that would be a big plus in customers minds and something Steam are already doing for it's customers:ie, allowing product keys bought from a different site to download and install that same product and run on Steam.
ED have already been paid the money for that same module so it shouldn't matter to ED that their module was bought on Steam and not in the ED Store?
Always keep your customers happy I say: "Were there's a will there's a way".