Generally that's what game companies do. Fans are generally ok with this, though not all modders are. The legality of it all is questionable of course, but unless someone ever challenges it, it is what it is. It's generally not financially worth it to challenge it, even if one wanted to. And that's the story with a great many things in the computer gaming world, and just the world in general.
I wouldn't sweat it either way. If you want to make a mod, make a mod. If you don't, don't. Just be prepared that Obsidian (or pretty much any other game company that makes a game you make a mod for) will want a piece of any $$$ pie, and very well may take the design from your mod and put it into their game.