Somehow I cannot stop thinking abt the scene of Book in the bullet train speeding past Pencil. I KNOW it doesn't have that much meaning, but what if it's meant to represent that Book, too, found her independence outside of Freesmart.
She has been the only remaining member of Freesmart for a while now, and she doesn't have anyone to rely on. Which miiiight cause her to feel disconnected from them: most of them are together in the WTF, going through the same adventures and stuff, whereas she's competing and surviving the challenges on her own. Yes, she does have Needle, but the latter doesn't value her nowhere as near as Book does.
Even though she won't realise it for a while, she did all of this alone. She got this far on her own (and, well, with the viewers' help), without the help of her team. Before I go on, I was going to say that she views a win for herself as a win for Freesmart. However, she mentions at the end of BFDIA 23 that she won for herself. And that it feels great. If you're crazy enough for this animated book (like me), it all points towards Book developing a sense of self. To her developing herself beyond Freesmart, to her discovering her own strengths.
Once all of this is over, it'll hit her that she went through vastly different experiences. That she wasn't during those shopping trips, the tornado that sucked up the WTFlings, or the round around the ooze on pig's yum. She isn't present in those fond memories, unlike her friends, who are all there. Add that onto her already distinct worldview, and you have the recipe for an (hypothetical) disconnection (and later fall-out) with Freesmart.












