#1: To me, it does not look like the built-in effect. The outlines seem too perfect to be generated automatically. But I think it's not handdrawn rotoscopy either: too many different frames to draw - and nobody would draw tiny extralines to make the outline nicer! (See timeframe 0:36-0:37)
Especially the scene in the streets (0:26-0:32) fills me with wonder.
#2&3: This is actually a second question. How was this morphing effect achieved? To me it often looks as if only a few keyframes were drawn by hand, and the inbetweens were morphed digitally. The last scene is an obvious one. (Start min1:26)
Was this done in After Effects? Are there any third party plugins to so this?