I actually forgot that DD had this fountain, shame on me, but I'm more or less certain that the Source mentioned then has nothing to do with the Source we have now. In fact, I actually believe they expanded on that detail that never had a conclusion (?), and made a big thing out of it. As you mentioned, it only became important in the two DOS games.
That's all fine and dandy, but doesn't explain why no one in DOS2 mentions the dragons as being behind the death of Lucian. It seemed like everyone KNEW that they were behind his disappearance, while no one knows that or thinks so in DOS2. Also doesn't explain where the Knights and Slayers went.
But... we don't know where Aleroth lies in relation to Reaper's Coast, do we? For all we know, they could be very far apart, thus created their unique mythos around Lucian's death. Though when I think about it, it doesn't make much sense, considering magic and all that fuss. Things would've gone around.