Well, there's a simple technical reason for it actually. In the N64 games, the moment Dracula revives after 100 years in 1852 (this is also made clear in the Japanese version), which doesn't match up with the dates used for other games in the timeline at all. I suppose you could just ignore that information, but I'm guessing it's one of the reason the game ended up removed from the storyline. If the setting of the games is a completely different world and not an alternative timeline, then one wouldn't have to worry about details like that. Secondly, which is just my personal preference, there really isn't any set-up for it. But this is just what I think, of course.
So since Cornell appears in Judgment, has a shared history with the characters, but IGA still insist Legacy of Darkness is a gaiden, I thought the most simple way to reconcile this is that a event involving Cornell, with strong similarities to the plot of Legacy of Darkness, happend in a somewhat similar fashion in the IGA timeline. This may or may not fall in line with his comment about "tweaking" old storylines. Of course, a split timeline is still an alternative way to handle the situation, but it does require a lot of explanation.