Even though I didn't write the OP, I will say why I think it there is a good chance it will turn out to be correct.
IMO, Harry doesn't have a clue how to raise his spirit child or maybe only one clue. Maggie can have more or less normal conversations with Bonnea because she is a child. She doesn't see anything unusual about interacting with a talking skull because Maggie doesn't have a frame of reference to inform her what Bonnea really is and how different Bonnea is from a mortal like herself. So Maggie treats Bonnea like a friend or younger sibling she's looking out for. Harry knows what Bonnea is and treats her with kid gloves. Near the beginning of Peace Talks Harry says that Bonea, "is someone to be carefully managed."
Managed, not raised. I suspect there is a problem with that single minded kind of thinking. I think Bonnea will need guidance; in some respects, just like any other child, but not exactly because she isn't a mortal and her potential for doing harm is so much greater. We all know Bonnea isn't a ticking bomb, she's wet dynamite. With the innate knowledge of a wizard and a fallen angel at her disposal and with the added difficulty Harry will have teaching a spirit of intellect about ethics and morality; if someone, something or a dangerous situation gives Bonnea the right push or wrong push at the right moment, things may go boom!
Harry probably wants to keep Bob as far away from Bonnea as possible, because Bob would want to help Bonnea and that could be extremely dangerous. However, my guess is Harry needs Bob's help. Harry needs to understand what it's like to be a child who is also a spirit of intellect, to help him make better decisions raising Bonnea. Bob's involvement will accelerate Bonnea's growth and when the right or wrong situation pops up to push Bonnea even further, she could go from zero to sixty.
P.S. At some point in the near future, Harry might need Bonnea to go from zero to sixty. Ignoring theoretical political alliances Harry might make in the future, without becoming an immortal himself or learning some powerful new magical techniques, it's difficult for me seeing Harry becoming much stronger or a more potent force than he already is. Bonnea's knowledge could be a real difference maker for Harry. Bonnea herself almost certainly has the potential to be more powerful than Bob or Bob's blue counterpart, evil Bob. If this doesn't happen in the next few books, I think it almost certainly will in the BAT.
