Completely agree, it's totally weird, but it's nice seeing the Endar Spire again even though it makes the retcon and whole KotOR story even more unbelievable, my only plausible suggestion is that Revan dreamed the Endar Spire's complete explosion while he was out, also dreaming about Bastila attacking Revan. More plausible than an firery ball of explosion in orbit leaving whole sections of the a ship intact, which as we know usually doesn't happen.