Perhaps, what has happened here is; the guide only covers one path through the game. So when they said to side with New Yevon, the guide assumes that's what you will choose. This decision, in turn, may affect minor things down the line, such as Isaaru not being in Zanarkand, and some dialog being different here and there. Which wouldn't have been different, had you chosen New Yevon. Do you think that this may have happened?

Either that, or that is just not a very good guide!