So we will have to rely on the steam users themselves to help us answer this question. Now asking the people at Steam if they removed any of the content is pointless as their tech support is almost non existent. This would also explain why the more advanced the legendary mod becomes the more of these issues arise. That would explain the different version numbers between the retail and steam versions of the game.
What if the people at Steam removed the unused assets from their versions to provide a faster download? I also know that some of these assets are used in the DS1_Legendary_Mod. Now I know that there is content in retail versions of all the various Dungeon Siege editions that exist, but are not active in the final release of the games. If a person has both the steam version of DS1 and DS2 they appear to report more of these issues than do people with just one of the steam versions. Missing or problematic ambient characters and shopkeepers, innkeepers. Why do I think this you ask? Because of missing objects, objects that float above where they should be.
I am starting to believe that there is content missing from the Steam versions of both DS1 and DS2. There is more than just the version number mismatch.