Hello!
I've been thinking a lot about why Tom would leave with Meg. Tom - like everyone else on this show is a mess. He seems desperate/lost and needs something/someone to anchor him somehow but everyone he turns to ends up betraying him somehow.
It starts when he goes to see his biological father (not for the first time) and is violently sent away, then the departure happens and his mother leaves him so he’s rejected by both parents. After that he starts grabbing on to anyone who will take him. He meets up with, and is used by Holy Wayne only to have him dump pregnant Christina on him and then she dumps him with the baby as soon as she can. He reunites with his mother only for her to use him in her agenda to save the GR by recruitment but that doesn't work so he starts giving out hugs for his mother’s cause and even when he tells her how it is affecting him she doesn’t care. Nobody wants him for him – only what he can do for them.
The Meg comes around. She isn’t blatantly asking anything from him (only tell your mom Meg says hi) and he is not used to that and he doesn’t know how to respond to her. She is going to Miracle so he goes with her to figure out what Meg wants (because everyone wants something). It’s a bonus that the only people in the show so far that haven’t tried to outright use him is Kevin and his sister and they are both in Miracle too.