Retail boxes come with both Steam & GOG versions to prevent that problem. It's the best solution we could think of.
I was just looking at what version to get, Steam or GOG, and noticed this thread. I'm amazed this is considered a best solution. It's put me off my purchase now and I think I'll wait until this is resolved. Even if I get the retail version (assuming it comes to Australia in retail stores) I'll still have to install it twice to find multiplayer from two separated player bases. That sucks.
It makes no sense that the Steam version can't connect to the DRM-free version. The programming is obviously there not to use Steamworks for multiplayer so why not just use it. You could even give Steam version the option of multiplayer using Steam ID usign Steamworks or using non-Steam multiplayer.
Sorry to put it bluntly but I don't think you found the best solution but the easy solution. Otherwise thank you for what looks like a great game I knew little about until I became a kickstarter for DOS and I hope it's a great success.