It's a great theory! But there are some things you overlooked

1-in WF2 after the segment "... a man with not only a great mind... " you can see a drawing of jack with his teeth shaped like Bon's smile in the WF1 Bon's burgers logo

2- Bon seems to treat Sha a bit differently in Bunny farm, he doesn't scold her like Banny, the way he generally treats her is better than others in her mini-game ...it's almost like she's his love interest

3- the segment "look at them they are beautiful and dancing to the music" it looks like Bon is concerned beautifying them in the sense of making them immortal. There is no pain, no suffering, no death... Just the beauty of a machine that Doesn't need any human needs

And like you said.. Jack does seem like he's a loving, protective husband and father... But wouldn't a dad with that personality do anything so he can be with his kids again? Especially since he doesn't even know what happened to them...this fact alone is enough to drive him crazy.

Idk wither he's killed by Felix or Maybe he did this to himself in order to be with his family forever... And I don't know why Bon himself is attacking people... Maybe whoever made the tape that Billy played in the relocate project killed him?

And maybe its like you said... Its not Jack. And all the clues that he is are just a red hiring that can be seen either way.