Ultima IX takes place in an alternate universe- one where certain events unfolded differently or possibly didn't happen at all.
This would explain certain details like why the Tapestry of Ages shows the Avatar in his clothes pre-Ultima 4, or why some sequence of events are repeated from earlier games. It would also explain the inconsistent details between this game and the previous ones.The cancelled Ultima X is still canon to Ultima
The Avatar casts Armageddon, destroying most of Britannia as its remains fly off into space. Is the Avatar going to die on the remains of Britannia, along with the Guardian? No, they will merge, recreating Britannia as Alucinor, reshaping the world with a new history. This was the plot of Ultima X, following the events of Ultima IX. The events still happen as the official ending and continuation of the Ultima series, but the game representing this story has not been published, because it was ultimately canceled.The Bob White plot is still canon
All of the details of the Bob White plot are still part of the story. Though they take place in the background and are not referenced in the game, the game presents the plot in broad strokes as an abridged version, for example, the ending is describing the Ascension process of merging light and dark with the Time Lord describing the context of this process to the Avatar at some point. The player doesn't get to see the conversation with the Time Lord or any of the other details because the Bob White plot is All There in the Manual. Lord Blackthorn in Ultima IX is a copy/clone created by the Guardian.
Borrowing a plot point from Ultima Online , the Guardian, like Exodus in Ultima Online, created a facsimile of Blackthorn (who even though himself to be the original), possibly as further psychological warfare against Lord British, as he did in the Bob White plot.It's also notable that in Ultima VII Part Two: Serpent Isle, Blackthorn was noted to fully find redemption, and materials cut from the game outright told he was deceased by this point.