He keeps Bob for himself. There are so many things he can do with such a resource. Just like Lasciel wants to have Bonea:
Bob is more powerful.
As I said before, what information does Bob have or power does Bob have that Anduriel couldn't provide? Anduriel has so much more that he is a whole different weight class by several orders of magnitude, even limited as he is, let alone unbound. Bob's most useful knowledge might be specific things he has learned about his various masters, and perhaps certain inherited knowledge from his creators (parents). Depending on who you believe those are, that's fairly significant. But it hardly seems likely Bob is the only spirit of intellect, not to mention he isn't even the top of the chain. That's probably the Archive in a sense. I am not talking about the mortal vessel (Ivy) but the spiritual mass that she carries. And as strong and intelligent as the Archive is...she did get captured by the Denarians after all.
I am interested to why you believe Bob is more powerful than Bonnie. Certainly he is more skillful at utilising his knowledge and powers, he's had centuries to learn whereas Bonnie is only getting started. But in terms of magical muscle, I'd tend to believe that Bonnie might be stronger. She has the knowledge base that Lash had, which is the knowledge that Lasciel had when she imprinted herself on Harry. It's true, we don't know how much knowledge she had. But she had enough that she seemed to think she was Lasciel, and knew enough secrets of the universe to do all sorts of scary things. Harry REALLY wasted his time with her, he could have learned so much without taking up her power. Instead he took the power and very little of her knowledge. I do acknowledge we haven't seen anything yet from Bonnie that shows her might (although we will I expect). She was expected to be able to go out an kill his loved ones accidentally were she birthed incorrectly. That alone right there says she is very strong. Maggie was protected by an extremely strong threshold and a cadre of angel guards, a former Knight of the Cross (although injured) and his battle-hardened wife, and a Foo Dog scion. Mab was certain Bonnie could get through all of that and kill Maggie, in attempting to connect with her. Bonnie would kill her by accident. Bob couldn't get past the first layer of those defences if he tried.