The issue of Konami magazine that came after the one that had the timeline said something like (and this a free translation): "That timeline was developed for Symphony of the Night, it was not made with Legends in mind." This was when the game was still in development, so already in the early stages somebody at Konami (probably IGA) protested against it being part of the timeline. I suppose the game wasn't "offically" removed when IGA became producer, which was in 2000. In the article you can see a timeline from that year that lists Legends as a "alternate universe story".