This is how I've understood it. The numbers are just for example, I have no clue how many will be on each layer.
Players 1-1,000 log in and are assigned "permanently" to layer 01. At least until layer is removed in Phase 02.
Players 1,001-2001 log in and are assigned "permanently" to layer 02. Etc. Until the player pool has slowed down and there's the final layer which will likely have people joining from then until the end of Phase 01.
Player 55 logs out for the day. The next day when he logs in he's still in layer 01. His friend is in layer 02. He invites his friend to a group and his friend is temporarily transported to layer 01 until the group is dissolved. If the friend in layer 02 invites player 55 to his group instead, player 55 will be transported to layer 02 until the group is dissolved. From what I can gather, the returning to original layers seems to happen when certain phasing "lines" are crossed in the world. This is why you have weird layering issues. At least that's my theory.