If he's drafted out of the NCAA, he can go to the Flyers (or ECHL/AHL) at any time. If he's drafted out of the Canadian junior ranks, he either makes the NHL club right away, or it's back to Canadian juniors for 2 years minimum. AHL and ECHL are not Canadian junior leagues.
The article points out that NIL has now made all previous Canadian league players (which were paid) now eligible for the NCAA, which they weren't before. That's the change. So once players reach 16 or 17, they are eligible for the Canadian junior leagues, and need to make a choice between them or the NCAA route. If you're a superstar or on the cusp, NCAA provides more flexibility.