It's not the beginning scenes, just the starting area.
Spoilered for those who haven't beaten the game [+]
The effects of the siphon were dampening Liz's power. Remember earlier in the game where she said that her ability has been getting weaker; that she used to be able to go where-/when-ever she wanted vice now only being able to open existing tears? She has that back, and effective omniscience due to being able to see all timelines. So, when Booker drops the flute, she transfers them to Rapture to put Songbird down, then uses it as a starting point for the rest of the ending mindscrew.
Spoilered for those who haven't beaten the game [+]
The effects of the siphon were dampening Liz's power. Remember earlier in the game where she said that her ability has been getting weaker; that she used to be able to go where-/when-ever she wanted vice now only being able to open existing tears? She has that back, and effective omniscience due to being able to see all timelines. So, when Booker drops the flute, she transfers them to Rapture to put Songbird down, then uses it as a starting point for the rest of the ending mindscrew.