I found none of what you describe, except for the HK-47 dialogs that make reference to the droid factory. As for incomplete quests, they are not. You can complete them alright. If you say that just because they stay in your log they are "incomplete" you are just being anal. And well, since that guide talks about a lot of stuff that didn't actually made it into the game, I wouldn't take it as gospel.
Oh, and another thing. Game developers don't endorse reverse engineering of their work. If you did that, and found stuff that you weren't supposed to, it's not their problem, it's yours.
But you are right. The case is closed. The game is what it is, and no amount of whining is going to change that. As I said before, deal with it and move on.