I would think maybe in this au, Scout knows that Spy's his Dad (he probably hears a French Lullaby and remembered someone singing that to him and connected the dots after a few weeks), but he's waiting for him to confess. Maybe he guilt trips Spy by being a great father to Phoebe and just tells everyone that he's a better Dad than his old man and Spy is just trying not to cry or flinch at the cruel words.
Although Scout has no obligation to offer Spy any forgiveness nor let Spy be a part of Phoebe's life, I think if he was open to letting Spy have a shot at being a better grandfather than he ever was a father, it could be a very healing experience for the both of them. That said Scout's still a thousand times better father than Spy ever was, and he has every right to rub that in.
I think Scout already knows, deep down. But if he hasn't figured it out by now, Reactor would have, and she wouldn't let Scout go oblivious. Spy seems deeply ashamed of his choices and if offered to him I doubt he'd let himself lose his last chance to make things right.