I think Jax getting this room only made her trauma worse and dug herself deeper into the closet

Apart from getting brain scanned during the lowest time of your life, being stuck in ridiculous cartoon body, you also get this room. Yes, maybe Jax actually likes this room deep down, but he was forced into living in it when he clearly wasn't ready to face that truth about himself and only serves as a reminder about his past.

"Ew, you like this room?? You're so stupid, how can you call yourself a man if you sleep here. If mom ever sees this room she's gonna laugh at your face again. But she can't, remember? Because she's dead. Because YOU killed her!"

And when Caine pulled Blue (i'm just gonna call it Blue) out his head, it remained a blue orb. That makes sense because we did see that Blue was still in early development before Caine ate him. Caine was a rough draft, but still had more work put into him, and I think that's what made him evolve himself equivalent to a human. Combined with Blue their power was practically godly in the digital world.

Blue is akin to a toddler. It never reached development where it grew to be a complex AI like Caine did. And Blue's simple consciousness of anger and ego was fighting against Caine's complexity of change and humility.