Just like the rest of the game, the lore is being reworked too. Again Yoshida's vision seems to clash with Tanaka's, so Tanaka's ideas and whatnot are getting the axe. The game is changing drastically, this is no different. With 2.0 I imagine everything will make sense together.

For new players they won't know that the lore has been changed and it'll all make perfect sense to them. Again these changes only seem bad to us because we've been exposed to the old, changing lore already.