The team still has access to the butterfly... Whatever. It's basically a room of requirement, so I think it isn't quite the house any more after endgame - it adapts to the needs of its occupants.
Is there still a butterfly? I don't get this question.
There are as many as there need to be - see above.
There are, but only P-users can open the door to Paradise, so they aren't a threat to the general public (provided Reizo doesn't start tossing people in next). However, there are still some loose-ends there so that people can organize post-game dungeon things if they so desire.