Well, it's one thing for mods to work for the modder, it's another for random people playing it. I assume all the assets in D:OS EE will still be in the files of D:OS2, though obviously not the reverse. Unless the modify assets from the EE for D:OS2, then there would be problems. Probably would be smart to make your own root templates at least, though doing that for everything would be a nightmare. And actually including all the models and whatnot in your mod release would bloat the file enormously.
D:OS2 could very easily have new engine features that make mods from the EE incompatible with it. They are probably spending a lot less time on brand new features, but I wouldn't be surprised to see some in development. We'll see on the 26th whether D:OS2 looks extremely different, or more of just a new campaign.
